bowtie2-build-l

name	bowtie2-build-l
description	Use when building large Bowtie 2 index files from reference sequences for alignment of reads to large genomes (>4 billion bases).
disable-model-invocation	true
user-invocable	true

bowtie2-build-l

Builds large-format Bowtie 2 index files (.bt2l extension) from FASTA reference sequences for use with bowtie2-align-l.

Quick Start

• Command: bowtie2-build-l [options] <reference_in> <bt2_index_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-build-l
• Full reference: See references/help.md for complete options

When To Use This Tool

• Use bowtie2-build-l when the reference is large enough that you need Bowtie 2 large-index output (.bt2l).
• It is appropriate when preparing references for bowtie2-align-l or a wrapper that resolves to the large-index path.
• Use it for one or more FASTA files, or with -c when sequences are provided directly on the command line.
• Most users should call bowtie2-build unless they intentionally need to force the large-index builder.

Common Patterns

# Build a large Bowtie 2 index from one FASTA
bowtie2-build-l ref.fa ref_large

# Build from multiple FASTA files
bowtie2-build-l ref1.fa,ref2.fa ref_large

# Use multiple threads during index construction
bowtie2-build-l --threads 8 ref.fa ref_large

# Build from literal reference sequence text
bowtie2-build-l -c ACGTACGT,GGGTTTAA ref_large

Recommended Workflow

1. Prepare your reference sequences in FASTA format (single or multiple files)
2. Run bowtie2-build-l <reference.fasta> <index_basename> to generate index files
3. Verify that six .bt2l files were created with the specified basename
4. Use the index basename with bowtie2 -x <index_basename> for alignment

Guardrails

• Consider using the bowtie2-build wrapper instead, as recommended by the tool warning
• Ensure sufficient memory/disk space; large references require significant resources during indexing
• Use --threads to parallelize builds on multi-core systems for faster processing
• The output basename should be passed later via -x without adding .bt2l suffixes manually