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agouti

Annotated Genome Optimization Using Transcriptome Information

angsd

Program for analysing NGS data.

batchqc

Provides Quality Control of sequencing samples by deducing if there is batch effect and adjusts for it.

bio-playground

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

biomarkdown

Markdown for learning bioinformatics

cafe

genometools

GenomeTools genome analysis system.

gitextensions

GitExtensions is a shell extension, a Visual Studio 2010-2015 plugin and a standalone Git repository tool.

glanet

GLANET: Genomic Loci ANnotation and Enrichment Tool

marvel

The MARVEL assembler

mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

mytestblog

test

ngs_data_processing

Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.

ngstools

Programs to analyse NGS data for population genetics purposes

paper-zhang2014

Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26

pym

Python for you and me book

rascaf

Scaffolding with RNA-seq read alignment

rsem

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

seqtk

Toolkit for processing sequences in FASTA/Q formats

soapdenovo-trans

SOAPdenovo-Trans, a de novo transcriptome assembler designed specifically for RNA-Seq. We evaluated its performance on transcriptome datasets from rice and mouse.

vcf2dis

VCF2Dis: A new simple and efficient software to calculate p-distance matrix based Variant Call Format

wormbase-pipeline

Sanger Wormbase Build Pipeline