Introduction

ebi-metagenomics/biosiftr is a bioinformatics pipeline that generates taxonomic and functional profiles for low-yield (shallow shotgun: < 10 M reads) short raw-reads using MGnify biome-specific genome catalogues as a reference.

The biome selection includes all the biomes available in the MGnify genome catalogues.

The main sections of the pipeline include the following ...

Mobilome Annotation Pipeline (former MoMofy)

Bacteria can acquire genetic material through horizontal gene transfer, allowing them to rapidly adapt to changing environmental conditions. These mobile genetic elements can be classified into three main categories: plasmids, phages, and integrative elements. Plasmids are mostly extrachromosmal; phages can be found extrachromosmal or as temperate phages (prophages); whereas integrons are stable inserted in the chromosome. Autonomous elements are ...