linxingchen Goto Github PK

agnostos-wf

aligngraph

Algorithm for secondary de novo genome assembly guided by closely related references

anhydeg

Database of anaerobic hydrocarbon degradation genes used for functional gene searching of metagenome data sets

astra

pyHMMer-based sequence search and retrieval tool.

bam2graph

figure out paired end links between contigs

bamcov

:boom: Quickly calculate and visualize sequence coverage in alignment files

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bathy16stree

Methods to make 16S rRNA gene tree of Bathyarchaeota and intermediate files

binf_toolkit

Handy scripts for routine bioinformatic analysis

bioconda-recipes

Conda recipes for the bioconda channel.

blast2ani

Garcia, S. L., Stevens, S. L. R., Crary, B., Martinez-Garcia, M., Stepanauskas, R., Woyke, T., Tringe, S. G., Andersson, S., Bertilsson, Malmstrom, R. R., McMahon, K. D. (ISMEJ). Genome level exploration of abundant and uncultivated freshwater bacteria reveals distinct and dynamic populations.

carter-and-olm-cell-2023---db-info

README for Zenodo archive associated with publication Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes

ccfind

circular complete sequence finder by detecting terminal redundancy

cenote-taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs

chainsaw

Rapidly Search and Hunt through Windows Forensic Artefacts

clinker

Gene cluster comparison figure generator

cobra

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

complete-python-3-bootcamp

Course Files for Complete Python 3 Bootcamp Course on Udemy

contig-extender

crispr

crispr analyses

crisprcasidentifier

Machine learning for accurate identification and classification of CRISPR-Cas systems

defense-finder

Systematic search of all known anti-phage systems.

domcycle

Identifying circular elements in complex microbial communities

dtr-phage-pipeline

fasta

basic scripts for fasta file

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

filter_reads.py

Filters BAM files created by bowtie2 for better read mapping. Use for genomes from metagenomes.

fix_assembly_errors

script for fixing assembly scaffolding errors

foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

friendsdontletfriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.