Segata Lab

lefse

panphlan

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

cmseq

Set of utilities on sequences and BAM files

metaml

viromeqc

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 respect to the expected prokaryotic markers abundances in reference metagenomes

metamlst

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

hclust2

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

cFMD

Public repository for cFMD - curatedFoodMetagenomicData

preprocessing

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

export2graphlan

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

repophlan

PanPhlAn_pangenome_exporter

MASTER-WP5-pipelines

pyphlan

FMT_Meta_Machine_Learning

metaclock

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

MetaRefSGB

MetaRefSGB_reports

viromedb

Scripts for the ViromeDB project

calculus_study_Lena_2021

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

diet_habits_microbiome_association

Repository with the command lines used to generate the microbiome meta-analyses and the microbiome machine learning in the vegetarian, vegan, omnivore diet comparison paper

inverse_var_weight

Object caller for stochastically dependent and independent effect-size and meta-analysis of correlations in Python

Msmithii_molecular_clocking

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

multidataset_machinelearning