Top 11 Python metagenomic Projects

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1. GTDBTk

   1 1 494 6.7 Python

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

   

2. SaaSHub

   www.saashub.com featured

   SaaSHub - Software Alternatives and Reviews. SaaSHub helps you find the best software and product alternatives

   

3. atlas

   2 2 379 7.4 Python

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

   

4. drep

   3 1 272 3.5 Python

   Rapid comparison and dereplication of genomes (by MrOlm)

   

5. metaGEM

   4 14 217 4.0 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

   

6. aviary

   5 3 86 7.3 Python

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

   

7. veba

   6 3 82 8.3 Python

   A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

   

8. kraken-biom

   7 1 50 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).

9. MOSCA

   8 12 35 4.4 Python

   Meta-Omics Software for Community Analysis (by iquasere)

   

10. GraphBin2

    9 1 33 8.7 Python

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

    

11. covid-19-signal

    10 1 31 6.2 Python

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

    

12. MetaRon

    11 1 7 2.1 Python

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

    

Python metagenomics related posts

• Metagenomic samples analysis: From taxonomic classification to reads mapping

  1 project | /r/bioinformatics | 9 Jun 2023

• Is Developing a Multi-omics Pipeline Feasable for a Masters Thesis?

  1 project | /r/bioinformatics | 19 May 2023

• Favorite Pipeline/Methods Figure

  4 projects | /r/bioinformatics | 24 Feb 2023

• Why bother reconstructing MAGs ?

  2 projects | /r/bioinformatics | 11 Jan 2023

• question about analysis of metagenome assembled genomes

  2 projects | /r/bioinformatics | 27 Sep 2022

• MetaQuast for assembling samples from complex communities

  1 project | /r/bioinformatics | 27 Jul 2022

• Finding BGCs from antiSMASH database in metagenomes

  1 project | /r/bioinformatics | 21 Jul 2022
• A note from our sponsor - SaaSHub
  www.saashub.com | 23 Jan 2025

  SaaSHub helps you find the best software and product alternatives Learn more →

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