Top 10 Python metagenomic Projects

GTDBTk

1 431 7.5 Python

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
atlas

2 346 9.3 Python

ATLAS - Three commands to start analyzing your metagenome data (by metagenome-atlas)
InfluxDB

www.influxdata.com sponsored

Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
drep

1 237 3.9 Python

Rapid comparison and dereplication of genomes (by MrOlm)
metaGEM

14 165 6.3 Python

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Project mention: Metagenomic samples analysis: From taxonomic classification to reads mapping | /r/bioinformatics | 2023-06-09

Maybe this workflow will be interesting to you: it assembles metagenomes, generates bins, and also creates metabolic models for predicting interactions within microbiomes 💎 https://github.com/franciscozorrilla/metaGEM

aviary

3 67 9.1 Python

A hybrid assembly and MAG recovery pipeline (and more!)

Project mention: what would you choose to detect specific genes in metagenomics data | /r/bioinformatics | 2023-06-12

Aviary is a good binning pipeline (there are others available), though perhaps more geared towards prokaryotes.

kraken-biom

1 43 0.0 Python

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
MOSCA

12 32 8.2 Python

Meta-Omics Software for Community Analysis (by iquasere)
WorkOS

workos.com sponsored

The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
covid-19-signal

1 30 5.5 Python

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
GraphBin2

1 27 7.8 Python

☯️🧬 Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs
MetaRon

1 6 1.8 Python

Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020).