subread-buildindex

name	subread-buildindex
description	Use when building an index from a reference sequence for Subread alignment tools.
disable-model-invocation	true
user-invocable	true

subread-buildindex

Quick Start

• Command: subread-buildindex -o <basename> <reference.fa[.gz]>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/subread-buildindex
• Version: 2.1.1
• Full reference: See references/help.md for detailed options and usage

When To Use This Tool

• Build the reference index required by subread-align and subjunc.
• Tune index layout for memory or speed with -F, -B, and -M.
• Create the index once per reference build, then reuse it across samples.

Common Patterns

# 1) Default index build
subread-buildindex -o ref_index genome.fa

# 2) Build from gzipped FASTA
subread-buildindex -o ref_index genome.fa.gz

# 3) Favor speed at the cost of larger memory/index size
subread-buildindex -o ref_index -F -B -M 16000 genome.fa

Recommended Workflow

1. Choose a stable basename for the index; downstream aligners refer to that basename with -i.
2. Build from the exact FASTA used for the project assembly and annotation.
3. Decide whether you want the default compact index or a larger full index with -F.
4. Verify the expected index files exist before aligning any sample.

Guardrails

• The required argument is -o <basename>; the reference FASTA comes after options as positional input.
• -F builds a full index that is larger on disk but can improve alignment behavior for some workloads.
• -B disables index splitting and can increase alignment memory use substantially.
• -M is the requested RAM budget in MB during index building; raise it explicitly for large genomes.