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angst

Analyzer of Gene and Species Trees

anvio

An analysis and visualization platform for 'omics data

biogo

biogo is a bioinformatics library for Go

blca

burst

An ultrafast optimal aligner for mapping large NGS data to large genome databases.

das_tool

DAS Tool

dotfiles

XMonad, acme plumb configuration files (OpenBSD/Slackware)

drep

Rapid comparison and dereplication of genomes

eggnog-mapper

Fast genome-wide functional annotation through orthology assignment

examples

example applications built using bíogo

external

bíogo external command interface repository

gatb-core

Core library of the Genome Analysis Toolbox with de-Bruijn graph

gleesso_pipeline

Inference of co-abundance graph for metagenomic species

gt-pro

hmmer

OpenBSD port of hmmer

krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

labtalks

Org-mode in reproducible research

latentstrainanalysis

Partitioning and analysis methods for large, complex sequence datasets

metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds

mlrepo

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

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.

mothur.github.io

wiki for the mothur software package

ncbi

bíogo ncbi utilities repository

org-transclusion

Emacs package to enable transclusion with Org Mode

phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

phyloseq-extended

Various customs functions written to enhance the base functions of phyloseq. Most of them are used in the formation "Métagénomique 16S" provided by the platforms Migale and Genotoul

prodigal

Prodigal Gene Prediction Software

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

pub_data

Programs, scripts used to generate figures in published work