Discover biocore/Platypus-Conquistador Open Source project

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

781

qiime

SortMeRNA: next-generation sequence filtering and alignment tool

285

sortmerna

C++

169

emp

Code repository of the Earth Microbiome Project.

Neural networks for microbe-metabolite interaction analysis

154

mmvec

American Gut open-access data and IPython notebooks

117

American-Gut

The Biological Observation Matrix (BIOM) Format Project

107

biom-format

Deblur is a greedy deconvolution algorithm based on known read error profiles.

deblur

Microbial analysis in TCGA data

tcga

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

gemelli

Vanilla regression methods for microbiome differential abundance analysis

songbird

compositional data analysis toolbox

gneiss

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

emperor

A fast and scalable phylogenetic tree viewer for microbiome data analysis

empress

Sample search by metadata and features

redbiom

unifrac

Recipes for bioinformatics analyses with scikit-bio

scikit-bio-cookbook

Robust Aitchison PCA from sparse count data

DEICODE

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

q2-qemistree

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

qurro

exploratory and interactive microbiome analyses based on heatmaps

calour

A QIIME 2 plugin for interaction with the Greengenes2 database

q2-greengenes2

Reference Phylogeny for Bacterial and Archaeal Genomes

wol

Bayesian Inferential Regression for Differential Microbiome Analysis

BIRDMAn

annotation pipeline for microbial genomes and metagenomes

micronota

Automated taxonomy decoration onto a tree

tax2tree

evident

Snakemake workflow for comparison of differential abundance ranks

qadabra

oecophylla

shotgun pipeline

Workflow for detecting genome-wide horizontal gene transfers

horizomer

Processing support for Greengenes2

greengenes2

Tools for developing and testing command line interfaces in Python.

pyqi

Python framework for controlling command-line applications.

burrito

Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests

pynast

Jupyter notebooks to assist with sample processing

metagenomics_pooling_notebook

A set of tools for delivering personal microbiome results to individuals participating in microbiome sequencing studies.

my-microbes

Filtering out false taxonomic hits from shotgun sequencing based on genome coverage

zebra_filter

Application controllers for command line bioinformatics applications

burrito-fillings

Elucidating sampling effort for microbial analysis studies

Evident-initial-demo

Multidimensional scaling algorithms for microbiology-ecology datasets.

mds-approximations

A private microservice to support The Microsetta Initiative

microsetta-private-api

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

conda-recipes

The website for the American Gut Project participant portal

american-gut-web

Default reference data files for use with QIIME.

qiime-default-reference

Request For Comments (RFCs) for scikit-bio.

scikit-bio-rfcs

labadmin

Administration website for the Knight Lab

Applying umap to microbiome data via QIIME2

q2-umap

Balanced parentheses succinct data structure in Python

improved-octo-waddle

descrete False Discovery Rate method

dsFDR

A tool for exploring biogeographical patterns

SitePainter

bayestime

Statistical and empirical subsampling of reference genomes

genome-subsampler

Aggregate genome coverage

micov

taxster: assigning taxonomy to organisms you've never even heard of

cmi-workshops

taxster

MPI-based sequence clusterer

PipeClust

microsetta-public-api

A public microservice to support The Microsetta Initiative

lab manager for plate maps and sequence flows

LabControl

RESTful interface into the American Gut data

american-gut-rest

unifrac-binaries

C++

biocore.github.io

CSS

q2-ili

QIIME2 plugin for `ili

q2-katharoseq

The Microsetta participant facing user interface

microsetta-interface

Jinja

qiime-workshops

Materials for biocore organized workshops

structural annotation pipeline for microbial genomes and metagenomes

microprot

Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal

mg-scripts

Emperor implementation in the SAGE2 framework

sage-emperor

A QIIME 2 plugin for assessing sample mislabeling and contamination

q2-mislabeled

A QIIME2 plugin for working with and processing American Gut data

q2-american-gut