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alignment-and-variant-calling-tutorial

basic walk-throughs for alignment and variant calling from NGS sequencing data

allhic

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

allhic_pipeline

Pipeline for Straightforward Usage of ALLHic

awesome-crispr

List of software/websites/databases/other stuff for genome engineering

bch709

Introduction to Bioinformatics

bio_scripts

Practical, reusable scripts for bioinformatics

biotools

A list of useful bioinformatics resources

class_2021

Statistical and computational analysis of the human genome

custom-repeat-library

Code for the Custom Repeat Library protocol as described: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Repeat_Library_Construction-Advanced

deeploc

Predicting protein subcellular localization using deep learning

deg_analysis

Flexible Gene Differential Expression Analysis

flair

Full-Length Alternative Isoform analysis of RNA

gene_map

Tool for converting between various gene ids

genelab-sampleprocessing

geta

harding-rna-sequencing-pipeline

A pipeline for analyzing RNA sequencing data for the Harding lab at WSU

helixer

Using Deep Learning to predict gene annotations

hmmerme

ice-plant-transcriptome-profiling

inpactor

Inpactor: Integrated and Parallel Analyzer and Classifier of LTR Retrotransposons for Large Genomes

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

lab

labwebsite

mcscanx

MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!

mutfinder_ems

A pipeline to identify causal mutations in EMS mutant

nchart

Creates an N-chart for comparing assembly lengths, including script for counting assembly lengths from a fasta file

paralleldotplot

ParaGrAl: Parallel graphic alignment of sequences. Addressing the comparison of sequences in the post-genomic era by high perfomance computing.

pbjelly

a fork of the gap-closing pipeline PBJelly

plantgenomicslab.github.io

planttf_identifier

podplot

Plot coverage or percent of total sequence as a function of minimum read length