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    54 repositories

    • MAGIC

      Public
      The Metagenome-Assembled Genome Inventory for Children (MAGIC)
      viromemetagenome-assembled-genomeskeystone-speciesearly-life-microbiomebacteriome
      0•1•0•0•Updated Oct 25, 2024Oct 25, 2024

    • quantpi

      Public
      Microbiome profiling
      Python
      •
      GNU General Public License v3.0
      •2•16•0•0•Updated Oct 16, 2024Oct 16, 2024

    • amdpi

      Public
      AMD: research power CPU
      Jupyter Notebook
      •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • metapi

      Public
      A general metagenomics data mining system focus on robust microbiome research
      Python
      •
      GNU General Public License v3.0
      •17•56•2•0•Updated Sep 14, 2024Sep 14, 2024

    • phanta

      Public
      Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
      Python
      •
      MIT License
      •9•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

    • qiimepi

      Public
      Snakemake version of QIIME2
      snakemake-workflowsamplicon-pipelineqiime2
      Python
      •0•1•0•0•Updated Apr 5, 2024Apr 5, 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•3•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

    • jobtk

      Public
      Some utils related with Sun Grid Engine and SLURM system
      Python
      •0•0•0•0•Updated Nov 22, 2022Nov 22, 2022

    • storepi

      Public
      More economical and efficient storage for sequencing data
      0•1•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•1•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

    • archpi

      Public
      Archaeology pieline for ancient genome and microbiome
      0•0•0•0•Updated Dec 29, 2021Dec 29, 2021

    • flupi

      Public
      Influenza viruses analysis pipeline
      0•0•0•0•Updated Dec 23, 2021Dec 23, 2021

    • scipi

      Public
      Single cell immune profiling pipeline
      0•0•0•0•Updated Dec 22, 2021Dec 22, 2021

    • camipi

      Public
      Upload data to CAMI community
      Python
      •0•0•0•0•Updated Mar 16, 2021Mar 16, 2021

    • dnbtk

      Public
      A toolkit to manage raw data from DNB sequencing platform
      Python
      •0•0•0•0•Updated Mar 12, 2021Mar 12, 2021

    • Mash

      Public
      Fast genome and metagenome distance estimation using MinHash
      C++
      •
      Other
      •91•0•0•0•Updated Mar 9, 2021Mar 9, 2021

    • inStrain

      Public
      Bioinformatics program inStrain
      Python
      •
      GNU General Public License v3.0
      •33•0•0•0•Updated Jan 21, 2021Jan 21, 2021