Novelty-inclusive microbial community profiling of shotgun metagenomes

Various scripts used at the EnvGen group, directed towards metagenomic analysis.

Metagenomics Workshop

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

bioBakery tools for meta'omic profiling

SAMSA pipeline, version 2.0. An open-source metatranscriptomics pipeline for analyzing microbiome data, built around DIAMOND and customizable reference databases.

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Assembly and binning of metagenomes

Assembly and annotation of metatranscriptomic or metagenomic data for prokaryotic, eukaryotic and viruses.

The is mostly a wrapper tool using phyloseq and microbiome R packages.

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

microbiome R package