bbmap

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.
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  # if packaged; else follow upstream

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