Name: Bowtie2 Align L
Author: vimalinx

Quick Start

When To Use This Tool

Use bowtie2-align-l when your reference was indexed in Bowtie 2 large-index format (.bt2l), typically for very large references.
It is appropriate for aligning single-end, paired-end, interleaved, or name-sorted unaligned BAM reads against that large index.
Use it when you specifically need the large-index binary, not the generic bowtie2 wrapper.
Most routine workflows should still prefer the bowtie2 wrapper unless you need to force the large-index executable directly.

Use bowtie2-align-l when your reference was indexed in Bowtie 2 large-index format (.bt2l), typically for very large references.
It is appropriate for aligning single-end, paired-end, interleaved, or name-sorted unaligned BAM reads against that large index.
Use it when you specifically need the large-index binary, not the generic bowtie2 wrapper.
Most routine workflows should still prefer the bowtie2 wrapper unless you need to force the large-index executable directly.