| name | bbmap |
| description | Fast splice-aware aligner and BBTools suite utilities (BBMerge, etc.). Use this skill when working with bbmap: installing, choosing parameters, running commands, interpreting outputs, or troubleshooting. Upstream: https://sourceforge.net/projects/bbmap/. For stage routing use tool-selection / metagenomics-workflow.
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| license | MIT |
| category | analysis-tools |
| tags | ["mapping","alignment","bbtools"] |
| upstream | https://sourceforge.net/projects/bbmap/ |
| stage | mapping |
BBMap
Upstream: BBMap
Citation
Bushnell, B. BBMap: a fast, accurate, splice-aware aligner. LBNL Report (2014). https://escholarship.org/uc/item/1h3515gn
See also docs/references.md.
Analytical thinking
Useful Swiss-army mapper/utilities; for standard metagenome coverage prefer Bowtie2/strobealign unless BBMap is already standardized in the lab.
How to run
conda install -c bioconda bbmap
bbmap.sh ref=contigs.fa in1=clean_1.fq.gz in2=clean_2.fq.gz \
out=temp/map/${id}.bam threads=16
Key parameters
| ref= | contigs | |
| out= | BAM/SAM | |
Decision notes
- Stage: mapping / utilities (BBTools suite)
- Prefer for specialized BBMerge/BBDuk tasks; for Illumina→contigs coverage prefer
strobealign / bowtie2
Related skills
bowtie2 · samtools · coverm · tool-selection · metagenomics-workflow
