Repositories list

• atmpi

  Public
  ASV-to-MAG Matching pipeline

  Python

  •0•0•0•0•Updated Mar 20, 2026Mar 20, 2026

• skillpi

  Public
  Working in progress (Don't use it)

  Python

  •0•0•0•0•Updated Mar 18, 2026Mar 18, 2026

• metapi

  Public
  A general metagenomics data mining system focus on robust microbiome research

  Python

  •

  GNU General Public License v3.0

  •19•60•2•0•Updated Mar 3, 2026Mar 3, 2026

• quantpi

  Public
  Microbiome profiling

  Python

  •

  GNU General Public License v3.0

  •4•15•0•0•Updated Nov 20, 2025Nov 20, 2025

• singpi

  Public
  0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• magpi

  Public
  0•0•0•0•Updated Nov 11, 2025Nov 11, 2025

• biotk

  Public
  Python

  •0•0•0•0•Updated Nov 6, 2025Nov 6, 2025

• qcpi

  Public
  0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

• dadapi

  Public
  Snakemake version of DADA2

  0•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• qiimepi

  Public
  Snakemake version of QIIME2

  snakemake-workflowsamplicon-pipelineqiime2

  snakemake-workflowsamplicon-pipelineqiime2

  Python

  •0•1•0•0•Updated Aug 6, 2025Aug 6, 2025

• MAGIC

  Public
  The Metagenome-Assembled Genome Inventory for Children (MAGIC)

  viromemetagenome-assembled-genomeskeystone-species+ 2

  viromemetagenome-assembled-genomeskeystone-speciesearly-life-microbiomebacteriome

  1•3•0•0•Updated Jun 24, 2025Jun 24, 2025

• jobtk

  Public
  Some utils related with Sun Grid Engine and SLURM system

  Python

  •0•0•0•0•Updated Feb 12, 2025Feb 12, 2025

• amdpi

  Public
  AMD: research power CPU

  Jupyter Notebook

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• phanta

  Public
  Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes

  Python

  •

  MIT License

  •11•0•0•0•Updated Sep 4, 2024Sep 4, 2024

• simpi

  Public
  Simulate metagenomics sequencing data for complex microbiome community of bacteriome, archaeome, virome, mycobiome, mobilome and resistome.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 28, 2024Jun 28, 2024

• strainpi

  Public
  A pipeline for identify strains from metagenomics data

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 21, 2024Mar 21, 2024

• rnapi

  Public
  RNA seq analysis pipeline

  Python

  •1•2•0•0•Updated Mar 12, 2024Mar 12, 2024

• gtdb-rev

  Public
  0•0•0•0•Updated Oct 12, 2023Oct 12, 2023

• callpi

  Public
  Calling SNP, SNV, CNV, and other genotyping information from metagenomics sequencing data

  Python

  •0•0•0•0•Updated Aug 11, 2023Aug 11, 2023

• mpsepi

  Public
  Microbiota Process and Visualization pipeline based on the MicrobiotaProcess R Package

  Python

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Mar 23, 2023Mar 23, 2023

• treepi

  Public
  Phylogenetic tree pipeline

  0•0•0•0•Updated Feb 7, 2023Feb 7, 2023

• growpi

  Public
  Microbial community grow rate profiling pipeline (WIP)

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 27, 2022Dec 27, 2022

• crisprpi

  Public
  0•0•0•0•Updated Dec 26, 2022Dec 26, 2022

• storepi

  Public
  More economical and efficient storage for sequencing data

  0•2•0•0•Updated Jul 15, 2022Jul 15, 2022

• journal-club

  Public
  0•0•0•0•Updated Jul 15, 2022Jul 15, 2022

• MetaVis

  Public
  high quality and reproducible visualization

  R

  •

  MIT License

  •2•0•0•0•Updated May 19, 2022May 19, 2022

• sshtk

  Public
  SSH toolkit

  Python

  •0•0•0•0•Updated Mar 22, 2022Mar 22, 2022

• crosspi

  Public
  Crosstalk of microbes, viruses and host

  0•0•0•0•Updated Jan 20, 2022Jan 20, 2022

• tbpi

  Public
  T/B cell repertoires profiling

  Python

  •0•0•0•0•Updated Jan 5, 2022Jan 5, 2022

• foldpi

  Public
  Snakemake version of AlphaFold

  0•0•0•0•Updated Dec 30, 2021Dec 30, 2021