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dumoar's Introduction

Beautiful Jekyll

xscode Gem Version

By Dean Attali ยท Demo

Beautiful Jekyll is a ready-to-use template to help you create a beautiful website quickly. Perfect for personal sites, blogs, or simple project websites. Check out a demo of what you'll get after just two minutes. You can also look at my personal website or my consulting website to see it in use, or see examples of websites other people created using this theme.

If you enjoy Beautiful Jekyll, please consider supporting me for over 5 years of development (and to unlock rewards!) โค

Table of contents

Features

Check out What's New? to see the latest features.

  • SIMPLE: The primary goal of Beautiful Jekyll is to allow literally anyone to create a website in a few minutes.
  • Modern: Uses the latest best practices and technologies to achieve nearly perfect scores on Google Chrome's Audit.
  • Mobile-first: Designed to look great on both large-screen and small-screen (mobile) devices.
  • Highly customizable: Many personalization settings such as changing the background colour/image, adding a logo.
  • Flexible usage: Use Beautiful Jekyll directly on GitHub or via a Ruby gem - choose the best development method for you.
  • Battle-tested: By using Beautiful Jekyll, you'll be joining 50,000+ users enjoying this theme since 2015.
  • SEO and social media support: Customize how your site looks on Google and when shared on social media.
  • Comments support: Add comments to any page using either Disqus, Facebook comments, Utterances, or Staticman.
  • Tags: Any blog post can be tagged with keywords, and an index page showing all the tags is automatically generated.
  • Analytics: Easily integrate Google Analytics, or other analytics platforms, to track visits to your website.
  • Photos support: Any page can have a full-width cover photo and thumbnail.
  • RSS: An RSS feed is automatically created, so you can even host a podcast easily with Beautiful Jekyll.

Sponsors ๐Ÿ†

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Become the first sponsor for Beautiful Jekyll and unlock special rewards!

Build your website in 3 steps

There's a very easy way to use this theme, and there's a hard way. For most people (including myself!), I suggest going the easy route. If you're an advanced user and want to tinker with the hard way (using ruby gems), then skip the easy way if you know what you're doing.

The easy way (recommended!)

Getting started is literally as easy as 1-2-3 ๐Ÿ˜„

Scroll down to see the steps involved, but here is a 40-second video just as a reference as you work through the steps. If you don't already have a GitHub account, you'll need to sign up.

Installation steps

1. Fork this project

Fork this project by clicking the Fork button at the top right corner of this page. Forking means that you now copied this entire project and all the files into your account.

2. Rename the project to <yourusername>.github.io

Click on Settings at the top (the cog icon) and on that page you'll have an option to rename the project (Repository name). This will create a website with the Beautiful Jekyll template that will be available at https://<yourusername>.github.io within a couple minutes (check out the FAQ if you want to use a different project name). If after a few minutes your website is still not ready, try making any edit to any file, just to force GitHub to re-build your site.

3. Customize your website settings

Edit the _config.yml file to change any settings you want. To edit the file, click on it to view the file and then click on the pencil icon to edit it (watch the video tutorial above if you're confused). The settings in the file are self-explanatory and I added comments inside the file to help you understand what each setting does. Any line that begins with a hashtag (#) is a comment, and the other lines are actual settings.

Note that in the video above I only edited one setting in the _config.yml file. You should actually go through the rest of the settings as well. Don't be lazy, go through all the settings!

4. Congratulations! You have a website!

After you save your changes to the _config.yml file (by clicking on Commit changes as the video tutorial shows), your website should be ready in a minute or two at https://<yourusername>.github.io. Every time you make a change to any file, your website will get rebuilt and should be updated in about a minute or so. Your website will be initialized with several sample blog posts and a couple other pages.

Note that this was the easy way to create your website, but it does come at a cost: when Beautiful Jekyll gains new features in the future, updating your website to include all the latest features is cumbersome. See the FAQ for help with upgrading in the future.

The hard way (using ruby gems)

If you followed the easy method above, then you already have your site and you can skip this section! If you want to use Beautiful Jekyll as a ruby gem instead, follow the advanced installation instructions. This is harder to set up initially, but it makes it super easy to keep your site up to date with Beautiful Jekyll when more features are added in the future.

Plans

Beautiful Jekyll is, and always will be, free. But if you want to remove the Beautiful Jekyll ad from your website, use a Dark Mode skin, unlock other special rewards, or simply support my development efforts, check out the different plans.

Add your own content

To add pages to your site, you can either write a markdown file (.md) or you can write an HTML file. It's much easier to write markdown than HTML, so I suggest you do that (here's a great tutorial if you need to learn markdown in 5 minutes).

To see an example of a markdown file, click on any file that ends in .md, for example aboutme.md. On that page you can see some nicely formatted text (there's a word in bold, a link, a few bullet points), and if you click on the pencil icon to edit the file, you'll see the markdown code that generated the pretty text. Very easy!

In contrast, look at tags.html. That's how your write HTML - not as pretty. So stick with markdown if you don't know HTML.

Any markdown or HTML file that you create will be available on your website under https://<yourusername>.github.io/<pagename>. For example, if you create a file about.md (or about.html) then it'll exist at https://<yourusername>.github.io/about.

Files you create inside the _posts directory will be treated as blog entries. You can look at the existing files there to get an idea of how to write blog posts. Note the format of the blog post files - they must follow the naming convention of YEAR-MONTH-DAY-title.md. After you successfully add your own post, you can delete the existing files inside _posts to remove the sample posts, as those are just demo posts to help you learn.

Customizing parameters for each page

One last important thing: In order to have your new pages use this template and not just be plain HTML pages, you must add YAML front matter to the top of each page:

---
---

This is where you'll be able to give each page some extra parameters (such as a title, a subtitle, an image, etc - below is a list of all parameters). Add any parameters you want between these two dashed lines, for example:

---
title: Contact me
subtitle: Here you'll find all the ways to get in touch with me
---

If you don't want to use any parameters on a page, you still need to use the two dashed lines. If you don't, then your file will be shown as-is without the Beautiful Jekyll template.

You can look at the top of aboutme.md as an example.

Important takeaway: ALWAYS add the YAML front matter, which is two lines of three dashes, to EVERY page. If you have any parameters, they go between the two lines.

Supported parameters

Below is a list of the parameters that Beautiful Jekyll supports (any of these can be added to the YAML front matter of any page). Remember to also look in the _config.yml file to see additional site-wide settings.

Main parameters

These are the basic YAML parameters that you are most likely to use on most pages.

Parameter Description
title Page or blog post title
subtitle Short description of page or blog post that goes under the title
tags List of tags to categorize the post. Separate the tags with commas and place them inside square brackets. Example: [personal, analysis, finance]
cover-img Include a large full-width image at the top of the page. You can either provide the path to a single image (eg. "/path/to/img") , or a list of images to cycle through (eg. ["/path/img1", "/path/img2"]). If you want to add a caption to an image, then the image should be provided as {"/path/to/img" : "Caption of image"}.
thumbnail-img For blog posts, if you want to add a thumbnail that will show up in the feed, use thumbnail-img: /path/to/image. If no thumbnail is provided, then cover-img will be used as the thumbnail. You can use thumbnail-img: "" to disable a thumbnail.
comments If you want do add comments to a specific page, use comments: true. Comments only work if you enable one of the comments providers (Facebook, disqus, staticman, utterances) in _config.yml file. Comments are automatically enabled on blog posts but not on other pages; to turn comments off for a specific post, use comments: false.

Parameters for SEO and social media sharing

These parameters let you control what information shows up when a page is shown in a search engine (such as Google) or gets shared on social media (such as Twitter/Facebook).

Parameter Description
share-title A title for the page. If not provided, then title will be used, and if that's missing then the site title (from _config.yml) is used.
share-description A brief description of the page. If not provided, then subtitle will be used, and if that's missing then an excerpt from the page content is used.
share-img The image to show. If not provided, then cover-img or thumbnail-img will be used if one of them is provided.

Less commonly used parameters

These are parameters that you may not use often, but can come in handy sometimes.

Parameter Description
readtime If you want a post to show how many minutes it will take to read it, use readtime: true.
show-avatar If you have an avatar configured in the _config.yml but you want to turn it off on a specific page, use show-avatar: false.
social-share By default, every blog post has buttons to share the page on social media. If you want to turn this feature off, use social-share: false.
nav-short By default, the navigation bar gets shorter after scrolling down the page. If you want the navigation bar to always be short on a certain page, use nav-short: true
gh-repo If you want to show GitHub buttons at the top of a post, this sets the GitHub repo name (eg. daattali/beautiful-jekyll). You must also use the gh-badge parameter to specify what buttons to show.
gh-badge Select which GitHub buttons to display. Available options are: [star, watch, fork, follow]. You must also use the gh-repo parameter to specify the GitHub repo.
last-updated If you want to show that a blog post was updated after it was originally released, you can specify an "Updated on" date.
layout What type of page this is (default is post for blog posts and page for other pages). See Page types section below for more information.

Advanced parameters

These are advanced parameters that are only useful for people who need very fine control over their website.

Parameter Description
footer-extra If you want to include extra content below the social media icons in the footer, create an HTML file in the _includes/ folder (for example _includes/myinfo.html) and set footer-extra to the name of the file (for example footer-extra: myinfo.html). Accepts a single file or a list of files.
before-content Similar to footer-extra, but used for including HTML before the main content of the page (below the title).
after-content Similar to footer-extra, but used for including HTML after the main content of the page (above the footer).
head-extra Similar to footer-extra, but used if you have any HTML code that needs to be included in the <head> tag of the page.
language HTML language code to be set on the page's <html> element.
full-width By default, page content is constrained to a standard width. Use full-width: true to allow the content to span the entire width of the window.
js List of local JavaScript files to include in the page (eg. /assets/js/mypage.js)
ext-js List of external JavaScript files to include in the page (eg. //cdnjs.cloudflare.com/ajax/libs/underscore.js/1.8.2/underscore-min.js). External JavaScript files that support Subresource Integrity (SRI) can be specified using the href and sri parameters eg.
href: "//code.jquery.com/jquery-3.1.1.min.js"
sri: "sha256-hVVnYaiADRTO2PzUGmuLJr8BLUSjGIZsDYGmIJLv2b8="
css List of local CSS files to include in the page
ext-css List of external CSS files to include in the page. External CSS files using SRI (see ext-js parameter) are also supported.

Page types

  • post - To write a blog post, add a markdown or HTML file in the _posts folder. As long as you give it YAML front matter (the two lines of three dashes), it will automatically be rendered like a blog post. Look at the existing blog post files to see examples of how to use YAML parameters in blog posts.
  • page - Any page outside the _posts folder that uses YAML front matter will have a very similar style to blog posts.
  • home - The home layout is meant to act as the homepage of your blog posts - it will display all your blog posts, sorted from newest to oldest. A file using the home layout must be named index.html (not index.md or anything else!).
  • minimal - If you want to create a page with minimal styling (ie. without the bulky navigation bar and footer), assign layout: minimal to the YAML front matter.
  • If you want to completely bypass the template engine and just write your own HTML page, simply omit the YAML front matter. Only do this if you know how to write HTML!

Featured users (success stories!)

Visit the Official website to see sample websites using Beautiful Jekyll.

If you'd like to showcase yourself and join this list, upgrading to the Individual plan will give you that publicity plus some other rewards!

FAQ and support

Visit the official FAQ page for answers to commonly asked questions.

Beautiful Jekyll is used by 50,000+ people with wildly varying degrees of web skills, so it's impossible to answer all the questions that may arise. For any question that's not specifically related to Beautiful Jekyll and is more about Jekyll or web development in general, the answer can often be found on Google, in the Jekyll documentation, or on the Jekyll support forum.

To receive support, select one of the different plans Beautiful Jekyll offers.

Contributions

Thank you to all past contributors. If you find any problems or would like to contribute in any way, feel free to create a pull request/open an issue/send me a message.

You can also contribute by becoming an official sponsor to help keep Beautiful Jekyll well-maintained.

Credits

This template was not made entirely from scratch. I'd like to give special thanks to Jekyll Now and Bootstrap Clean Blog, from whom I've taken several ideas initially.

I'd also like to thank Dr. Jekyll's Themes, Jekyll Themes, and another Jekyll Themes for featuring Beautiful Jekyll in their Jekyll theme directories.

dumoar's People

Contributors

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Watchers

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dumoar's Issues

Confirm two lanes per sample for MBD-BS data

The MBD-BS directory on Sedna has two subdirectories, "4416" and " 4417" with two fastq.gz files per sample (R1 and R2). The filenames in both subdirectories are identical but file sizes differ, for example:

[lspencer@sedna MBDseq_UOdata]$ du -sh 4416/CH01_06* 4417/CH01_06*
617M    4416/CH01_06_S1_L001_R1_001.fastq.gz
551M    4416/CH01_06_S1_L001_R2_001.fastq.gz
721M    4417/CH01_06_S1_L001_R1_001.fastq.gz
704M    4417/CH01_06_S1_L001_R2_001.fastq.gz

I presume each sample was run across two lanes but it's weird that all file names include "L001". @mgavery were samples run across two lanes?

Cool acronym

First things first, we need a showstopper of an acronym for this project. Add your suggestions as comments in this issue.

(I can change this repo's name to the acronym once identified)

Determine Mitochondria Sequence in Genome

Based on first pass I believe it is likely in unscaffolded portion - ??

Blast Approach comparing M mag mitochondria sequence to M mag genome

Make blast index

/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ../data/PGA_assembly.fasta \
-dbtype nucl \
-out ../results/04-mito-hunt/PGA_assembly

Blasting Mitochondria feature fasta to genome

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-query ../data/Mmag-mito-features.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_01.tab \
-evalue 1E-20 \
-num_threads 48 \
-max_target_seqs 10 \
-outfmt 6

cat ../results/04-mito-hunt/mit-genome_blastn_01.tab

## lcl|NC_050675.1_gene_8   PGA_scaffold16__99_contigs__length_13714835 85.409  281 39  2   214 493 12231568    12231289    2.68e-76    291
## lcl|NC_050675.1_gene_14  contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 1.67e-110   403
## lcl|NC_050675.1_gene_28  contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   1.62e-152   544
## lcl|NC_050675.1_gene_29  contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 7.18e-155   549
## lcl|NC_050675.1_gene_30  contig_4859_pilon__unscaffolded 100.000 68  0   0   1   68  664 597 2.28e-28    126
## lcl|NC_050675.1_gene_32  contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    0.0 647
## lcl|NC_050675.1_gene_34  contig_4859_pilon__unscaffolded 98.485  66  1   0   1   66  3686    3751    1.31e-25    117
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  74.652  718 119 45  61  755 30054   29377   6.60e-67    259
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  74.652  718 119 45  61  755 100314  99637   6.60e-67    259
## lcl|NC_050675.1_gene_38  contig_4678_pilon__unscaffolded 73.561  556 89  40  227 755 22881   23405   6.89e-37    159
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 89.442  663 41  15  137 788 1694    2338    0.0 809
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 93.333  75  4   1   784 858 3712    3785    4.44e-22    110
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  80.894  738 96  27  136 858 30895   30188   1.33e-151   540
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  80.894  738 96  27  136 858 101155  100448  1.33e-151   540
## lcl|NC_050675.1_gene_39  contig_444_pilon___fragment_11__unscaffolded    79.383  713 102 29  137 829 55975   56662   1.06e-127   460
## lcl|NC_050675.1_gene_39  contig_91_pilon__unscaffolded   79.296  710 104 27  137 829 27935   27252   1.38e-126   457
## lcl|NC_050675.1_gene_39  contig_5765_pilon__unscaffolded 85.621  459 34  26  374 828 8339    8769    1.78e-125   453
## lcl|NC_050675.1_gene_39  contig_6518_pilon__unscaffolded 78.969  718 106 28  137 837 721 32  8.28e-124   448
## lcl|NC_050675.1_gene_39  PGA_scaffold22__59_contigs__length_10008237 78.711  667 87  30  137 788 9907893 9908519 1.09e-107   394
## lcl|NC_050675.1_gene_39  PGA_scaffold22__59_contigs__length_10008237 93.333  75  4   1   784 858 9909891 9909964 4.44e-22    110
## lcl|NC_050675.1_gene_39  contig_4401_pilon___fragment_5__unscaffolded    78.004  491 92  12  137 615 37291   36805   1.14e-77    294
## lcl|NC_050675.1_gene_39  contig_396_pilon__unscaffolded  78.481  395 65  12  160 539 79648   80037   1.51e-61    241
## lcl|NC_050675.1_gene_39  contig_4678_pilon__unscaffolded 94.845  97  5   0   762 858 21929   22025   7.27e-35    152
## lcl|NC_050675.1_gene_40  contig_4859_pilon__unscaffolded 100.000 71  0   0   1   71  6392    6322    5.25e-30    132
## lcl|NC_050675.1_cds_YP_009926422.1_3 PGA_scaffold16__99_contigs__length_13714835 85.409  281 39  2   214 493 12231568    12231289    2.68e-76    291
## lcl|NC_050675.1_cds_YP_009926426.1_7 contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 1.67e-110   403
## lcl|NC_050675.1_cds_YP_009926429.1_10    contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   1.62e-152   544
## lcl|NC_050675.1_cds_YP_009926430.1_11    contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 7.18e-155   549
## lcl|NC_050675.1_cds_YP_009926431.1_12    contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    0.0 647

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-query ../data/Mmag-mito-features.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_02.tab \
-evalue 1E-50 \
-num_threads 48 \
-max_target_seqs 10 \
-outfmt 6

cat ../results/04-mito-hunt/mit-genome_blastn_02.tab

## lcl|NC_050675.1_gene_8   PGA_scaffold16__99_contigs__length_13714835 85.409  281 39  2   214 493 12231568    12231289    2.68e-76    291
## lcl|NC_050675.1_gene_14  contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 1.67e-110   403
## lcl|NC_050675.1_gene_28  contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   1.62e-152   544
## lcl|NC_050675.1_gene_29  contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 7.18e-155   549
## lcl|NC_050675.1_gene_32  contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    0.0 647
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 89.442  663 41  15  137 788 1694    2338    0.0 809
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  80.894  738 96  27  136 858 30895   30188   1.33e-151   540
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  80.894  738 96  27  136 858 101155  100448  1.33e-151   540
## lcl|NC_050675.1_gene_39  contig_444_pilon___fragment_11__unscaffolded    79.383  713 102 29  137 829 55975   56662   1.06e-127   460
## lcl|NC_050675.1_gene_39  contig_91_pilon__unscaffolded   79.296  710 104 27  137 829 27935   27252   1.38e-126   457
## lcl|NC_050675.1_gene_39  contig_5765_pilon__unscaffolded 85.621  459 34  26  374 828 8339    8769    1.78e-125   453
## lcl|NC_050675.1_gene_39  contig_6518_pilon__unscaffolded 78.969  718 106 28  137 837 721 32  8.28e-124   448
## lcl|NC_050675.1_gene_39  PGA_scaffold22__59_contigs__length_10008237 78.711  667 87  30  137 788 9907893 9908519 1.09e-107   394
## lcl|NC_050675.1_gene_39  contig_4401_pilon___fragment_5__unscaffolded    78.004  491 92  12  137 615 37291   36805   1.14e-77    294
## lcl|NC_050675.1_gene_39  contig_396_pilon__unscaffolded  78.481  395 65  12  160 539 79648   80037   1.51e-61    241
## lcl|NC_050675.1_cds_YP_009926422.1_3 PGA_scaffold16__99_contigs__length_13714835 85.409  281 39  2   214 493 12231568    12231289    2.68e-76    291
## lcl|NC_050675.1_cds_YP_009926426.1_7 contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 1.67e-110   403
## lcl|NC_050675.1_cds_YP_009926429.1_10    contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   1.62e-152   544
## lcl|NC_050675.1_cds_YP_009926430.1_11    contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 7.18e-155   549
## lcl|NC_050675.1_cds_YP_009926431.1_12    contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    0.0 647

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/Mmag-mito-features.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_03.tab \
-evalue 1E-20 \
-num_threads 48 \
-max_target_seqs 1 \
-outfmt 6

## Warning: [blastn] Examining 5 or more matches is recommended

cat ../results/04-mito-hunt/mit-genome_blastn_03.tab

## lcl|NC_050675.1_gene_8   PGA_scaffold16__99_contigs__length_13714835 85.211  284 40  2   211 493 12231571    12231289    4.48e-84    316
## lcl|NC_050675.1_gene_14  contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 2.94e-108   396
## lcl|NC_050675.1_gene_28  contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   2.79e-149   533
## lcl|NC_050675.1_gene_29  contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 4.69e-151   536
## lcl|NC_050675.1_gene_30  contig_4859_pilon__unscaffolded 100.000 68  0   0   1   68  664 597 1.49e-27    123
## lcl|NC_050675.1_gene_32  contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    9.61e-180   633
## lcl|NC_050675.1_gene_33  contig_4859_pilon__unscaffolded 97.015  67  2   0   1   67  3619    3685    2.63e-24    113
## lcl|NC_050675.1_gene_34  contig_4859_pilon__unscaffolded 98.485  66  1   0   1   66  3686    3751    7.35e-25    115
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  72.840  729 139 21  46  755 30065   29377   1.12e-103   381
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  72.840  729 139 21  46  755 100325  99637   1.12e-103   381
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 84.731  799 83  15  1   788 1568    2338    0.0 859
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 93.333  75  4   1   784 858 3712    3785    6.63e-22    110
## lcl|NC_050675.1_gene_40  contig_4859_pilon__unscaffolded 100.000 71  0   0   1   71  6392    6322    3.77e-29    129
## lcl|NC_050675.1_cds_YP_009926422.1_3 PGA_scaffold16__99_contigs__length_13714835 85.211  284 40  2   211 493 12231571    12231289    4.48e-84    316
## lcl|NC_050675.1_cds_YP_009926426.1_7 contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 2.94e-108   396
## lcl|NC_050675.1_cds_YP_009926429.1_10    contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   2.79e-149   533
## lcl|NC_050675.1_cds_YP_009926430.1_11    contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 4.69e-151   536
## lcl|NC_050675.1_cds_YP_009926431.1_12    contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    9.61e-180   633

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/Mmag-mito-features.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_04.tab \
-evalue 1E-50 \
-num_threads 48 \
-max_target_seqs 10 \
-outfmt 6

cat ../results/04-mito-hunt/mit-genome_blastn_04.tab

## lcl|NC_050675.1_gene_8   PGA_scaffold16__99_contigs__length_13714835 85.211  284 40  2   211 493 12231571    12231289    4.48e-84    316
## lcl|NC_050675.1_gene_14  contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 2.94e-108   396
## lcl|NC_050675.1_gene_28  contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   2.79e-149   533
## lcl|NC_050675.1_gene_29  contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 4.69e-151   536
## lcl|NC_050675.1_gene_32  contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    9.61e-180   633
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  72.840  729 139 21  46  755 30065   29377   1.12e-103   381
## lcl|NC_050675.1_gene_38  contig_185_pilon__unscaffolded  72.840  729 139 21  46  755 100325  99637   1.12e-103   381
## lcl|NC_050675.1_gene_38  contig_4678_pilon__unscaffolded 71.067  553 108 13  227 755 22881   23405   2.17e-68    265
## lcl|NC_050675.1_gene_38  contig_5718_pilon__unscaffolded 74.584  421 83  9   1   420 3857    4254    9.21e-67    259
## lcl|NC_050675.1_gene_38  PGA_scaffold22__59_contigs__length_10008237 74.584  421 83  9   1   420 9910036 9910433 9.21e-67    259
## lcl|NC_050675.1_gene_39  contig_5718_pilon__unscaffolded 84.731  799 83  15  1   788 1568    2338    0.0 859
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  77.829  875 138 22  1   858 31023   30188   0.0 655
## lcl|NC_050675.1_gene_39  contig_185_pilon__unscaffolded  77.829  875 138 22  1   858 101283  100448  0.0 655
## lcl|NC_050675.1_gene_39  contig_444_pilon___fragment_11__unscaffolded    76.596  846 152 24  1   829 55846   56662   8.57e-160   567
## lcl|NC_050675.1_gene_39  contig_6518_pilon__unscaffolded 76.023  855 149 23  1   837 848 32  2.99e-159   565
## lcl|NC_050675.1_gene_39  contig_91_pilon__unscaffolded   78.843  709 109 19  137 829 27935   27252   5.41e-156   554
## lcl|NC_050675.1_gene_39  PGA_scaffold22__59_contigs__length_10008237 75.467  803 132 24  1   788 9907767 9908519 5.78e-143   511
## lcl|NC_050675.1_gene_39  contig_5765_pilon__unscaffolded 78.510  698 89  32  145 828 8119    8769    1.55e-137   494
## lcl|NC_050675.1_gene_39  contig_4401_pilon___fragment_5__unscaffolded    73.267  707 111 20  137 829 37291   36649   2.16e-110   404
## lcl|NC_050675.1_gene_39  contig_396_pilon__unscaffolded  73.609  557 108 15  1   542 79508   80040   3.66e-82    310
## lcl|NC_050675.1_gene_39  contig_6427_pilon__unscaffolded 76.485  421 77  9   137 545 14880   14470   2.81e-77    293
## lcl|NC_050675.1_cds_YP_009926422.1_3 PGA_scaffold16__99_contigs__length_13714835 85.211  284 40  2   211 493 12231571    12231289    4.48e-84    316
## lcl|NC_050675.1_cds_YP_009926426.1_7 contig_2968_pilon__unscaffolded 99.107  224 2   0   1   224 41  264 2.94e-108   396
## lcl|NC_050675.1_cds_YP_009926429.1_10    contig_4859_pilon__unscaffolded 99.333  300 2   0   1   300 300 1   2.79e-149   533
## lcl|NC_050675.1_cds_YP_009926430.1_11    contig_4859_pilon__unscaffolded 100.000 297 0   0   1   297 590 294 4.69e-151   536
## lcl|NC_050675.1_cds_YP_009926431.1_12    contig_4859_pilon__unscaffolded 99.717  353 1   0   1   353 3109    3461    9.61e-180   633

Using Complete Mito genome

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ../data/Mmag_mito.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_05.tab \
-evalue 1E-20 \
-num_threads 48 \
-max_target_seqs 10 \
-outfmt 6

cat ../results/04-mito-hunt/mit-genome_blastn_05.tab

## NC_050675.1  contig_2968_pilon__unscaffolded 85.161  3511    384 79  35709   39160   264 3696    0.0 3751
## NC_050675.1  contig_2968_pilon__unscaffolded 85.706  3267    356 74  35016   38235   495 3697    0.0 3553
## NC_050675.1  contig_2968_pilon__unscaffolded 85.284  3085    316 68  36630   39658   259 3261    0.0 3335
## NC_050675.1  contig_2968_pilon__unscaffolded 84.932  2336    259 57  35016   37313   1414    3694    0.0 2453
## NC_050675.1  contig_2968_pilon__unscaffolded 85.367  2139    218 43  37559   39658   265 2347    0.0 2339
## NC_050675.1  contig_2968_pilon__unscaffolded 84.632  1386    168 35  35016   36383   2336    3694    0.0 1423
## NC_050675.1  contig_2968_pilon__unscaffolded 84.647  1205    120 29  38475   39658   265 1425    0.0 1268
## NC_050675.1  contig_2968_pilon__unscaffolded 90.409  782 56  11  1   770 1239    2013    0.0 1040
## NC_050675.1  contig_2968_pilon__unscaffolded 88.761  783 68  12  1   770 319 1094    0.0 980
## NC_050675.1  contig_2968_pilon__unscaffolded 88.348  781 70  9   1   770 2159    2929    0.0 977
## NC_050675.1  contig_2968_pilon__unscaffolded 90.096  626 52  7   1   623 3075    3693    0.0 828
## NC_050675.1  contig_2968_pilon__unscaffolded 87.832  452 47  8   35016   35462   3250    3698    1.99e-149   539
## NC_050675.1  contig_2968_pilon__unscaffolded 99.242  264 2   0   8152    8415    1   264 2.96e-128   468
## NC_050675.1  contig_2968_pilon__unscaffolded 86.939  245 27  4   39417   39658   264 506 6.98e-73    285
## NC_050675.1  contig_2968_pilon__unscaffolded 77.129  411 68  14  34625   35020   956 1355    2.97e-71    279
## NC_050675.1  contig_2968_pilon__unscaffolded 76.773  409 70  12  34627   35020   1877    2275    2.97e-71    279
## NC_050675.1  contig_2968_pilon__unscaffolded 76.773  409 70  12  34627   35020   2793    3191    2.97e-71    279
## NC_050675.1  contig_2968_pilon__unscaffolded 84.699  183 23  4   34840   35020   256 435 1.18e-44    191
## NC_050675.1  contig_2932_pilon__unscaffolded 84.969  1284    144 25  36771   38038   1257    7   0.0 1378
## NC_050675.1  contig_2932_pilon__unscaffolded 83.551  1301    150 30  37692   38972   1257    1   0.0 1305
## NC_050675.1  contig_2932_pilon__unscaffolded 83.180  1302    162 35  35840   37124   1262    1   0.0 1255
## NC_050675.1  contig_2932_pilon__unscaffolded 83.923  1188    152 30  35016   36188   1164    1   0.0 1182
## NC_050675.1  contig_2932_pilon__unscaffolded 84.615  1053    118 16  38616   39658   1260    242 0.0 1137
## NC_050675.1  contig_2932_pilon__unscaffolded 87.931  696 60  14  80  765 1261    580 0.0 836
## NC_050675.1  contig_2932_pilon__unscaffolded 89.815  432 40  3   1   431 429 1   3.37e-159   572
## NC_050675.1  contig_2932_pilon__unscaffolded 77.506  409 65  13  34627   35020   709 313 1.64e-74    289
## NC_050675.1  contig_2932_pilon__unscaffolded 82.812  256 39  5   35016   35269   253 1   1.75e-61    246
## NC_050675.1  contig_2932_pilon__unscaffolded 91.071  112 9   1   39547   39658   1263    1153    8.52e-34    154
## NC_050675.1  contig_4859_pilon__unscaffolded 99.125  686 3   1   20794   21479   1   683 0.0 1209
## NC_050675.1  contig_4859_pilon__unscaffolded 87.040  733 53  15  23567   24279   3048    3758    0.0 865
## NC_050675.1  contig_4859_pilon__unscaffolded 74.661  442 63  15  33080   33476   6321    6758    1.54e-68    269
## NC_050675.1  contig_4859_pilon__unscaffolded 100.000 144 0   0   31006   31149   4874    5017    7.96e-66    260
## NC_050675.1  contig_4859_pilon__unscaffolded 70.029  684 173 20  37341   38008   15219   15886   5.03e-62    249
## NC_050675.1  contig_4859_pilon__unscaffolded 73.759  423 82  14  23022   23428   2398    2807    1.64e-55    226
## NC_050675.1  contig_4859_pilon__unscaffolded 83.871  217 22  6   22160   22373   1003    1209    2.44e-53    219
## NC_050675.1  contig_4859_pilon__unscaffolded 68.640  625 168 20  36475   37088   15279   15886   2.14e-41    179
## NC_050675.1  contig_4859_pilon__unscaffolded 68.132  637 159 25  38316   38937   15279   15886   5.74e-36    161
## NC_050675.1  contig_4859_pilon__unscaffolded 69.149  470 118 14  8   464 15506   15961   2.44e-34    156
## NC_050675.1  contig_4859_pilon__unscaffolded 74.694  245 51  9   34716   34955   15312   15550   2.78e-27    132
## NC_050675.1  contig_4859_pilon__unscaffolded 72.481  258 59  8   36489   36743   9285    9533    1.76e-23    121
## NC_050675.1  contig_4859_pilon__unscaffolded 71.942  278 53  13  37396   37663   9271    9533    7.47e-22    114
## NC_050675.1  contig_185_pilon__unscaffolded  74.076  1813    331 53  29386   31147   29377   31101   0.0 1038
## NC_050675.1  contig_185_pilon__unscaffolded  74.076  1813    331 53  29386   31147   99637   101361  0.0 1038
## NC_050675.1  contig_5718_pilon__unscaffolded 83.829  841 93  17  30279   31107   2338    1529    0.0 866
## NC_050675.1  contig_5718_pilon__unscaffolded 74.956  571 107 15  29721   30283   4254    3712    5.72e-93    351
## NC_050675.1  contig_2928_pilon__unscaffolded 87.524  521 57  7   37003   37518   4   521 6.09e-175   623
## NC_050675.1  contig_2928_pilon__unscaffolded 85.822  529 59  11  35147   35671   5   521 1.86e-162   581
## NC_050675.1  contig_2928_pilon__unscaffolded 84.990  513 62  10  38846   39348   1   508 3.85e-152   547
## NC_050675.1  contig_2928_pilon__unscaffolded 84.130  523 73  8   37919   38435   1   519 1.64e-150   543
## NC_050675.1  contig_2928_pilon__unscaffolded 83.673  539 65  13  36063   36596   1   521 1.99e-149   538
## NC_050675.1  contig_2928_pilon__unscaffolded 86.017  472 49  7   309 770 4   468 1.99e-149   538
## NC_050675.1  contig_444_pilon___fragment_11__unscaffolded    75.647  928 175 27  30238   31147   56662   55768   6.51e-162   580
## NC_050675.1  contig_6518_pilon__unscaffolded 75.244  921 167 26  30230   31131   32  910 3.37e-159   572
## NC_050675.1  contig_91_pilon__unscaffolded   75.328  916 163 28  30238   31131   27252   28126   5.00e-157   564
## NC_050675.1  PGA_scaffold22__59_contigs__length_10008237 75.030  845 142 26  30279   31107   9908519 9907728 1.87e-143   518
## NC_050675.1  PGA_scaffold22__59_contigs__length_10008237 74.956  571 107 15  29721   30283   9910433 9909891 5.72e-93    351

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-query ../data/Mmag_mito.fa \
-db ../results/04-mito-hunt/PGA_assembly \
-out ../results/04-mito-hunt/mit-genome_blastn_06.tab \
-evalue 1E-20 \
-num_threads 48 \
-max_target_seqs 10 \
-outfmt 6

cat ../results/04-mito-hunt/mit-genome_blastn_06.tab

## NC_050675.1  contig_2968_pilon__unscaffolded 85.434  3515    367 103 35709   39160   264 3696    0.0 3520
## NC_050675.1  contig_2968_pilon__unscaffolded 85.885  3273    339 90  35016   38235   495 3697    0.0 3371
## NC_050675.1  contig_2968_pilon__unscaffolded 85.636  3084    307 97  36630   39658   259 3261    0.0 3116
## NC_050675.1  contig_2968_pilon__unscaffolded 85.171  2340    253 74  35016   37316   1414    3698    0.0 2313
## NC_050675.1  contig_2968_pilon__unscaffolded 85.701  2140    209 66  37559   39658   265 2347    0.0 2167
## NC_050675.1  contig_2968_pilon__unscaffolded 84.748  1390    159 42  35016   36383   2336    3694    0.0 1343
## NC_050675.1  contig_2968_pilon__unscaffolded 85.145  1205    114 43  38475   39658   265 1425    0.0 1173
## NC_050675.1  contig_2968_pilon__unscaffolded 90.537  782 55  12  1   770 1239    2013    0.0 1016
## NC_050675.1  contig_2968_pilon__unscaffolded 88.903  784 65  15  1   770 319 1094    0.0 946
## NC_050675.1  contig_2968_pilon__unscaffolded 88.875  782 64  17  1   770 2159    2929    0.0 941
## NC_050675.1  contig_2968_pilon__unscaffolded 90.256  626 51  9   1   623 3075    3693    0.0 809
## NC_050675.1  contig_2968_pilon__unscaffolded 87.832  452 47  8   35016   35462   3250    3698    6.39e-145   523
## NC_050675.1  contig_2968_pilon__unscaffolded 99.242  264 2   0   8152    8415    1   264 5.04e-131   477
## NC_050675.1  contig_2932_pilon__unscaffolded 85.404  1288    134 35  36770   38038   1259    7   0.0 1288
## NC_050675.1  contig_2932_pilon__unscaffolded 84.402  1263    134 47  37727   38972   1217    1   0.0 1182
## NC_050675.1  contig_2932_pilon__unscaffolded 83.879  1284    146 48  35860   37124   1242    1   0.0 1168
## NC_050675.1  contig_2932_pilon__unscaffolded 84.131  1191    144 37  35016   36188   1164    1   0.0 1110
## NC_050675.1  contig_2932_pilon__unscaffolded 85.133  1056    107 34  38616   39658   1260    242 0.0 1035
## NC_050675.1  contig_2932_pilon__unscaffolded 88.379  697 55  20  80  765 1261    580 0.0 815
## NC_050675.1  contig_2932_pilon__unscaffolded 90.069  433 37  6   1   431 429 1   6.30e-155   556
## NC_050675.1  contig_2932_pilon__unscaffolded 91.743  109 8   1   39550   39658   1260    1153    1.25e-32    150
## NC_050675.1  contig_4859_pilon__unscaffolded 99.125  686 3   2   20794   21479   1   683 0.0 1230
## NC_050675.1  contig_4859_pilon__unscaffolded 89.174  702 34  28  23600   24279   3077    3758    0.0 837
## NC_050675.1  contig_4859_pilon__unscaffolded 100.000 144 0   0   31006   31149   4874    5017    1.19e-67    267
## NC_050675.1  contig_4859_pilon__unscaffolded 85.321  218 17  12  22160   22373   1003    1209    5.65e-51    211
## NC_050675.1  contig_4859_pilon__unscaffolded 83.590  195 24  7   33242   33431   6522    6713    2.06e-40    176
## NC_050675.1  contig_4859_pilon__unscaffolded 81.166  223 28  10  23022   23241   2398    2609    1.24e-37    167
## NC_050675.1  contig_4859_pilon__unscaffolded 100.000 73  0   0   33080   33152   6321    6393    3.50e-28    135
## NC_050675.1  contig_5718_pilon__unscaffolded 89.442  663 41  15  30279   30930   2338    1694    0.0 809
## NC_050675.1  contig_5718_pilon__unscaffolded 76.348  575 92  30  29721   30283   4254    3712    3.30e-68    268
## NC_050675.1  contig_185_pilon__unscaffolded  76.489  1595    250 84  29386   30931   29377   30895   0.0 752
## NC_050675.1  contig_185_pilon__unscaffolded  76.489  1595    250 84  29386   30931   99637   101155  0.0 752
## NC_050675.1  contig_2928_pilon__unscaffolded 87.739  522 54  10  37003   37518   4   521 2.87e-168   601
## NC_050675.1  contig_2928_pilon__unscaffolded 86.226  530 55  16  35147   35671   5   521 1.75e-155   558
## NC_050675.1  contig_2928_pilon__unscaffolded 86.681  473 44  13  309 770 4   468 6.43e-140   507
## NC_050675.1  contig_2928_pilon__unscaffolded 84.411  526 69  11  37919   38436   1   521 2.31e-139   505
## NC_050675.1  contig_2928_pilon__unscaffolded 84.259  540 60  19  36063   36596   1   521 8.32e-139   503
## NC_050675.1  contig_3489_pilon__unscaffolded 86.621  441 42  16  37083   37514   433 1   2.35e-129   472
## NC_050675.1  contig_3489_pilon__unscaffolded 84.564  447 46  18  35227   35665   434 3   2.40e-114   422
## NC_050675.1  contig_3489_pilon__unscaffolded 86.154  390 29  17  390 765 433 55  4.04e-107   398
## NC_050675.1  contig_3489_pilon__unscaffolded 83.447  441 53  16  38003   38432   433 2   1.88e-105   392
## NC_050675.1  contig_3489_pilon__unscaffolded 81.718  454 56  16  36146   36592   434 1   8.87e-94    353
## NC_050675.1  contig_444_pilon___fragment_11__unscaffolded    79.383  713 102 29  30238   30930   56662   55975   5.08e-126   460
## NC_050675.1  contig_91_pilon__unscaffolded   79.296  710 104 27  30238   30930   27252   27935   6.57e-125   457
## NC_050675.1  contig_5765_pilon__unscaffolded 85.621  459 34  26  30239   30693   8769    8339    8.50e-124   453

Decide on version of genome to use

Seems like a few options for genome.

Full (scaffolds and contigs) - filename: PGA_assembly.fasta

Full - filtered (scaffolds and contigs): PGA_assembly.fasta.filtered.renamed.fa?

Scaffolds

Scaffolds filtered


What does filtered mean?


My vote is for scaffolds only

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