Obtaining MAGs (Metagenome-Assembled Genomes) from shotgun metagenomic sequencing data

On this link you will find a pipeline to obtain Metagenome-Assembled-Genomes(MAGs) from shotgun metagenomic sequencing data and a quality evaluation. You will need:

1. Access to a high-performance computing cluster.
2. A computer with administrator permission where you can access a UNIX terminal.
3. Shotgun metagenomic sequencing reads whose quality you already approve.

Instructions for the use of this pipeline

The pipeline contains a script that should be run in the cluster and additional commands to be run in the cluster and in the local computer. When you run the script it creates a colection of scripts adapted to the information of your sample. If you use the same cluster I used (Mazorka Langebio Cinvestav Mexico) the required software is already installed (latest versions on March 2021), but if you are using a different machine make sure it has the required software and adapt the script to the way it runs jobs.

Software that must be installed in the cluster

The numbers show the version I used, if you use a different version make sure it is compatible with the rest of the pipeline.

SPAdes 3.10.1

kraken 2.0.7

Braken 2.0

bowtie2 2.3.5.1

samtools 1.9

bwa 0.7.15

bamtools 2.4.1

minimap2 2.12

CheckM 1.1.3

hmmer 3.1b2

Prodigal 2.6.2

Software that must be installed in the local computer

VAMB