SnakeMAGs v1.1.1

In this version we corrected a bug observed when host genome filtering was not required.

SnakeMAGs v1.1.0

We are happy to announce the release of SnakeMAGs v1.1.0 which features two major improvements.

The first one, we implemented a new rule to detect and discard chimeric and contaminated genomes using the GUNC tool. It is optional, the user can choose to apply or not this treatment to its genomes.

The second one, at the bins quality filtering step, the user can choose if he wants to keep the bins above a minimum completion rate (by default 50%, but it can be adjusted) and below a maximum contamination rate (by default 10%, but it can be adjusted) or if he decides to filter bins according to the a quality score (completion-5*contamination >= 50), as defined in Parks et al. (2017) Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol 2, 1533–1542 https://doi.org/10.1038/s41564-017-0012-7.

SnakeMAGs

SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available for Linux.

SnakeMAGs

SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available for Linux.

v1.0.0

SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of SnakeMAGs is to process Illumina data from raw reads to metagenome-assembled genomes (MAGs). SnakeMAGs is efficient, easy to handle and flexible to different projects. The workflow is CeCILL licensed, implemented in Snakemake (run on multiple cores) and available for Linux.