bowtie2-build-s

name	bowtie2-build-s
description	Use when building Bowtie 2 index files from reference sequences for short-read alignment.
disable-model-invocation	true
user-invocable	true

bowtie2-build-s

Quick Start

• Command: bowtie2-build-s [options] <reference_in> <bt2_index_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-build-s
• Reference: references/help.md

When To Use This Tool

• Use bowtie2-build-s when building a standard Bowtie 2 small index (.bt2) for ordinary reference sizes.
• It is appropriate for FASTA input files or literal reference sequences supplied with -c.
• Use it when you specifically want to force the small-index builder rather than let the generic wrapper decide.
• In most routine workflows, bowtie2-build is still the preferred entry point unless you need direct control over the binary choice.

Common Patterns

# Build a standard Bowtie 2 index from one FASTA
bowtie2-build-s ref.fa ref

# Build from multiple FASTA files
bowtie2-build-s ref1.fa,ref2.fa ref

# Parallelize index construction
bowtie2-build-s --threads 8 ref.fa ref

# Build from literal sequence strings
bowtie2-build-s -c ACGTACGT,GGGTTTAA ref

Recommended Workflow

1. Prepare reference sequences in FASTA format
2. Run bowtie2-build-s <reference.fasta> <output_basename> to build the index
3. Verify index files were created with the specified basename
4. Use the generated index with bowtie2 -x <basename> for read alignment

Guardrails

• The tool recommends using the bowtie2-build wrapper script instead of this direct executable
• Use --threads <int> to parallelize index construction on multi-core systems
• Generated indexes are compatible with Bowtie v1.2.3 and later
• The basename passed to downstream aligners should omit any .bt2 suffix