bowtie2-build

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

bowtie2-build

Quick Start

• Command: bowtie2-build [options]* <reference_in> <bt2_index_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-build
• Version: 2.5.5
• Full reference: see references/help.md

When To Use This Tool

• Build a Bowtie2 index from FASTA reference sequence(s).
• Create the .bt2 files required by bowtie2.
• Rebuild the index when the reference assembly changes.
• Use before any Bowtie2 alignment job that lacks an existing index prefix.

Common Patterns

# 1) Basic Bowtie2 index build
bowtie2-build reference.fa ref_index

# 2) Multi-threaded build
bowtie2-build --threads 8 reference.fa ref_index

# 3) Force a large index
bowtie2-build --large-index reference.fa ref_index

Recommended Workflow

1. Build from the exact FASTA that the project will align against.
2. Choose a stable index basename and keep it consistent in pipeline configs.
3. Verify the .bt2 outputs exist before launching alignment jobs.
4. Document whether --large-index was used if the reference is unusually large.

Guardrails

• reference_in can be one FASTA or a comma-separated list of FASTA files.
• The index basename controls both directory and prefix; make sure the target path is writable.
• -c means reference sequences are on the command line, which is uncommon for real genomes.
• --large-index changes index format and should be used deliberately.