Assembly, binning and annotation of metagenomes

About 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 ...

Workflow (hybrid) metagenomic assembly and binning + GEMs

Accepts both Illumina and Long reads (ONT/PacBio)

• Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1

• Workflow LongRead Quality: https://workflowhub.eu/workflows/337

• Kraken2 taxonomic classification of FASTQ reads

• SPAdes/Flye (Assembly)

• QUAST (Assembly quality report)

Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)

• Metabat2/MaxBin2/SemiBin
• DAS Tool
• CheckM ...

Workflow for Metagenomics binning from assembly

Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file

Summary

• MetaBAT2 (binning)
• MaxBin2 (binning)
• SemiBin (binning)
• DAS Tool (bin merging)
• EukRep (eukaryotic classification)
• CheckM (bin completeness and contamination)
• BUSCO (bin completeness)
• GTDB-Tk (bin taxonomic classification)

Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default

**All tool CWL ...