2 items tagged with 'binning'.
Work-in-progress
Workflow (hybrid) metagenomic assembly and binning + GEMs
Accepts both Illumina and Nanopore
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Workflow Illumina Quality: https://workflowhub.eu/workflows/336?version=1
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Workflow LongRead Quality: https://workflowhub.eu/workflows/337
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Kraken2 taxonomic classification of FASTQ reads
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SPAdes/Flye (Assembly)
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QUAST (Assembly quality report)
Workflow binnning https://workflowhub.eu/workflows/64?version=11 (optional)
- Metabat2/MaxBin2/SemiBin
- DAS Tool
- CheckM
- BUSCO
- GTDB-Tk ...
Created: 14th Jun 2022 at 09:14, Last updated: 2nd Feb 2023 at 15:05
Work-in-progress
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 ...
Created: 15th Oct 2020 at 14:55, Last updated: 2nd Nov 2022 at 15:29