Pinned Repositories
assembly_finder
snakemake-powered cli to download genomes using NCBI datasets
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/.
locus2genoplotr
Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
MeSS
Snakemake pipeline for simulating shotgun metagenomic samples
microbiome_shotgun_pipeline
Snakemake pipeline for shotgun metagenomics
mummer2circos
Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
TPutils
zAMP
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
zDB
zDB: comparative bacterial genomics made easy
metagenlab's Repositories
metagenlab/mummer2circos
Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments
metagenlab/zDB
zDB: comparative bacterial genomics made easy
metagenlab/MeSS
Snakemake pipeline for simulating shotgun metagenomic samples
metagenlab/assembly_finder
snakemake-powered cli to download genomes using NCBI datasets
metagenlab/locus2genoplotr
Plot bacterial gene maps and genome comparison plots from command line with genoPlotR and GenomeDiagram
metagenlab/zAMP
zAMP is a bioinformatic pipeline designed for convenient, reproducible and scalable amplicon-based metagenomics
metagenlab/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/.
metagenlab/chlamdb
chlamdb.ch website code
metagenlab/TPutils
metagenlab/GENCOV
metagenlab/microbiome_shotgun_pipeline
Snakemake pipeline for shotgun metagenomics
metagenlab/updated_simulate_PCR
Corrected version of simulate_PCR (https://doi.org/10.1186/1471-2105-15-237)
metagenlab/MASRES
metagenlab/nanopore
metagenlab/benchmark-MeSS-CAMISIM
Nextflow pipeline to benchmark two shotgun metagenomic communities simulators
metagenlab/zAMPExplorer
zAMPExplorer
metagenlab/BioVx
The Extended BioV suite of programs (fully written in Python)
metagenlab/blast2profile
metagenlab/core_genome_phylogeny
Build a phylogeny with FastTree based on a concatenated alignment of 103 marker genes identified with checkM.
metagenlab/extractmag
Extract MAG of a specific taxon of interest from metagenome assembly
metagenlab/filterSAM
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
metagenlab/MeSS-figures
Supplemental code for reproducing MeSS paper figures
metagenlab/metagenlab_libs
metagenlab/MGE_identifier
metagenlab/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
metagenlab/rnaseq
Rnaseq pipeline