Gapped short-read alignment to contigs/genomes for coverage used in binning and abundance. Use when indexing assemblies, mapping cleaned PE reads, choosing sensitivity presets, QC of BAM rates, or preparing depths for MetaBAT2/CoverM/BASALT. Upstream: https://github.com/BenLangmead/bowtie2. Alternatives: strobealign, bwa-mem2. Always pair with samtools.
