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10x

admix_from_vcf

Run admixture on VCF files using python (and a perl script from snpeff)

allpath_ec

angsd

Program for analysing NGS data.

angsd-wrapper

Utilities for analyzing next generation sequencing data

annotation

arcs

Scaffold genome sequence assemblies using 10x Genomics data

assembly

assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

assign

awesome-python-applications

💿 Free software that works great, which also happens to be open-source Python.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

bamscripts

bamtobw

Convert BAM files to bigWig files with a simple command

bingo

biocode

Bioinformatics code libraries and scripts

bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics

bioinformatics-training

Bioinformatics training resources

bioinformatics_blogs

Blog bioinformatics

bionano

bionano_hybrid_na12878

bioperl

Local install

blasr

This is an unsupported fork of the PacBio blasr aligner. It contains my (very beta) optimizations and new functionality. It may disappear at any time.

breakseq

canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.

cdhit

Automatically exported from code.google.com/p/cdhit

chm1_scripts

circfinder

A pipeline to map junction reads for circular intronic RNAs (ciRNAs)

circos