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
QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- DAS Tool
- CheckM ...
Workflow for Metagenomics binning from assembly
Minimal inputs are: Identifier, assembly (fasta) and a associated sorted BAM file
- 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 ...