Type: Nextflow
Creators: No author provided, Hadrien Gourlé, Daniel Straub, Sabrina Krakau
Submitter: WorkflowHub Bot
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
- Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
- FastQC (control)
- fastp (quality trimming)
- kraken2 (taxonomy)
- bbmap contamination filter
- Workflow Longread Quality:
- NanoPlot (control)
- filtlong (quality trimming)
- kraken2 (taxonomy)
- minimap2 contamination filter
- Kraken2 taxonomic classification of FASTQ reads
- SPAdes/Flye (Assembly)
- Pilon/Medaka/PyPolCA (Assembly polishing)
- QUAST (Assembly ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
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 ...
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