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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