metagenlab

mummer2circos

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

zDB

zDB: comparative bacterial genomics made easy

MeSS

Snakemake pipeline for simulating shotgun metagenomic samples

assembly_finder

snakemake-powered cli to download genomes using NCBI datasets

locus2genoplotr

Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram

zAMP

zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics

chlamdb

chlamdb.ch website code

diag_pipelines

Pipelines dealing with high throughput sequencing data for microbiology diagnostic procedures. Documentation available at http://metagenlabdiag-pipelines.readthedocs.io/en/latest/ and Docker images at https://hub.docker.com/r/metagenlab/diag_pipelines/.

TPutils

GENCOV

microbiome_shotgun_pipeline

Snakemake pipeline for shotgun metagenomics

updated_simulate_PCR

Corrected version of simulate_PCR (https://doi.org/10.1186/1471-2105-15-237)

MASRES

nanopore

BioVx

The Extended BioV suite of programs (fully written in Python)

blast2profile

core_genome_phylogeny

Build a phylogeny with FastTree based on a concatenated alignment of 103 marker genes identified with checkM.

extractmag

Extract MAG of a specific taxon of interest from metagenome assembly

metagenlab_libs

MGE_identifier

MultiQC

Forking MultiQC in order to add to the parsing of qualimap results the extraction of the "General Error Rate". Will PR back there once performed

rnaseq

Rnaseq pipeline