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@SegataLab

Segata Lab

The computational metagenomics lab at the Dep. CIBIO, University of Trento

Popular repositories

  1. lefse Public

    Python 40 33

  2. panphlan Public

    PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

    Python 25 6

  3. cmseq Public

    Set of utilities on sequences and BAM files

    Python 17 5

  4. metaml Public

    Python 16 9

  5. viromeqc Public

    ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome. The score is calculated with respec…

    Python 9

  6. hclust2 Public

    Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.

    Python 7

Repositories

  • Python 3 1 1 0 Updated Apr 12, 2022
  • lefse Public
    Python 40 MIT 33 9 1 Updated Feb 15, 2022
  • export2graphlan Public

    Conversion software tool for producing both annotation and tree files for GraPhlAn

    Python 6 MIT 4 2 0 Updated Feb 2, 2022
  • preprocessing Public

    Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination

    Python 2 MIT 1 0 0 Updated Jan 26, 2022
  • panphlan Public

    PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

    Python 25 MIT 6 5 0 Updated Nov 3, 2021
  • cmseq Public

    Set of utilities on sequences and BAM files

    Python 17 MIT 5 2 1 Updated Oct 27, 2021
  • metaclock Public

    A python package for assisting to reconstruct time-tree at the strain level using contemporary and ancient metagenomes.

    Python 1 AGPL-3.0 0 0 0 Updated Sep 17, 2021
  • calculus_study_Lena_2021 Public

    This repo contains scripts for reproducing results reported in the calculus study, Lena et al., 2021

    Python 0 0 0 0 Updated Jun 23, 2021
  • Msmithii_molecular_clocking Public

    Code available for Marsha et al. 2021 - "Reconstruction of ancient microbial genomes from the human gut"

    Python 0 0 0 0 Updated Mar 17, 2021
  • metamlst Public

    MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.

    Python 6 MIT 0 0 0 Updated Jan 18, 2021

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