ekopylova

OTU-clustering

Scripts for benchmarking and comparison of short read OTU clustering tools available in QIIME

sortmerna

This is ongoing development of SortMeRNA. For the latest release, see http://bioinfo.lifl.fr/RNA/sortmerna/.

sortmedna

Development version of SortMeDNA

benchmarks

biom-format

The Biological Observation Matrix (BIOM) Format Project

burrito-fillings

Application controllers for command line bioinformatics applications

Complete-Striped-Smith-Waterman-Library

conda-recipes

conda recipes for bioinformatic tools like blast+, infernal, etc.

deblur

deblurring

distance-method

Python implementation of the Distance Method HGT search algorithm

emp

Data, code and analysis results for the Earth Microbiome Project.

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

hgt_analysis

Scripts for HGT analysis

MultiQC_TestData

Test data for MultiQC. See https://github.com/ewels/MultiQC

NINJA-OPS

Ninja Is Not Just Another OTU Picking Solution

OrthoFinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"

phylomizer

PhylomeDB automated pipeline for reconstructing high-quality phylogenetic tree

qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

qiime-deploy

Tool to easily install QIIME on Linux systems

qiime-deploy-conf

configuration files to be used with the qiime-deploy packages

scikit-bio

Core objects, functions and statistics for working with biological data in Python.

script_bin

A collection of potentially useful scripts

short-read-tax-assignment

A repository for storing code and data related to a systematic comparison of short read taxonomy assignment tools

tcga

TCGA analysis

tcga-1

Microbial analysis in TCGA data

WGS-HGT

Workflow for detecting genome-wide horizontal gene transfers