metagenlab Goto Github PK

assembly_finder

snakemake-powered cli to download genomes using NCBI datasets

biovx

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

blast2profile

chlamdb

chlamdb.ch website code

core_genome_phylogeny

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

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/.

extractmag

Extract MAG of a specific taxon of interest from metagenome assembly

gencov

locus2genoplotr

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

masres

mess

Snakemake pipeline for simulating shotgun metagenomic samples

metagenlab_libs

mge_identifier

microbiome_shotgun_pipeline

Snakemake pipeline for shotgun metagenomics

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

mummer2circos

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

nanopore

rnaseq

Rnaseq pipeline

tputils

updated_simulate_pcr

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

zamp

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

zdb

zDB: comparative bacterial genomics made easy