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calculus_study_lena_2021

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

cfmd

Public repository for cFMD - curatedFoodMetagenomicData

cmseq

Set of utilities on sequences and BAM files

export2graphlan

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

fmt_meta_machine_learning

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.

lefse

master-wp5-pipelines

metaclock

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

metaml

metamlst

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

metarefsgb

metarefsgb_reports

msmithii_molecular_clocking

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

multidataset_machinelearning

panphlan

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

panphlan_pangenome_exporter

preprocessing

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

pyphlan

repophlan

viromedb

Scripts for the ViromeDB project

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