Top 22 metagenomic Open-Source Projects

• MMseqs2

  4 1,259 7.7 C

  MMseqs2: ultra fast and sensitive search and clustering suite

  

• megahit

  1 558 0.0 C++

  Ultra-fast and memory-efficient (meta-)genome assembler

• InfluxDB

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• dada2

  1 449 4.3 R

  Accurate sample inference from amplicon data with single nucleotide resolution

• GTDBTk

  1 433 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)

  

• SqueezeMeta

  1 335 6.6 C

  A complete pipeline for metagenomic analysis

• training-material

  1 294 10.0 HTML

  A collection of Galaxy-related training material

  

• SaaSHub

  www.saashub.com featured

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• drep

  1 237 3.9 Python

  Rapid comparison and dereplication of genomes (by MrOlm)

• mag

  2 182 9.4 Nextflow

  Assembly and binning of metagenomes

  

• 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

• eager

  1 124 7.6 Nextflow

  A fully reproducible and state-of-the-art ancient DNA analysis pipeline

  

• DNAnalyzer

  4 123 8.1 Java

  Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools

Project mention: I'm approaching 1000 followers! | dev.to | 2023-06-13

P.S. If you haven't checked out my latest project, DNAnalyzer, please do so! It's a groundbreaking open source tool that brings the power of machine learning to DNA analysis. You can find it on GitHub or read more about it here on dev.to. I would love to hear your feedback and suggestions on how to make it better and more useful for everyone.

• aviary

  3 67 9.0 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.

• Metabuli

  1 62 9.0 C++

  Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

  

Project mention: Genomic sequence classification based on k-mers distribution | /r/bioinformatics | 2023-12-04

• 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)

• 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.

• virnet

  1 29 0.0 Jupyter Notebook

  VirNet: A deep attention model for viral reads identification

• 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.

• bracken_plot

  2 5 5.9 R

  A Shiny app for taxonomic abundance visualization

• Metadbgwas

  3 0 5.7 JavaScript

  Beginig of the expansion of DBGWAS to a metagenomic scale.

• SaaSHub

  www.saashub.com featured

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

  

metagenomics related posts

• what would you choose to detect specific genes in metagenomics data

  2 projects | /r/bioinformatics | 12 Jun 2023

• 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
• A note from our sponsor - InfluxDB
  www.influxdata.com | 3 May 2024

  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. Learn more →

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