bowtie2-inspect-l

name	bowtie2-inspect-l
description	Use when you need to inspect or extract information from a Bowtie 2 large index (.bt2l) file, including reference sequence names, lengths, or FASTA sequences.
disable-model-invocation	true
user-invocable	true

bowtie2-inspect-l

Quick Start

• Command: bowtie2-inspect-l <bt2_base>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/bowtie2-inspect-l
• Full reference: See references/help.md for complete options and details

When To Use This Tool

• Use bowtie2-inspect-l when you know the target index is a Bowtie 2 large index (.bt2l) and want to inspect it directly.
• It is useful for checking reference names, emitting a summary, or reconstructing FASTA from a large index without relying on wrapper auto-detection.
• Use it when troubleshooting large-index-specific behavior or when the generic inspector is not explicit enough about which index flavor to read.
• In normal usage, the bowtie2-inspect wrapper is usually preferable.

Common Patterns

# Summarize a large Bowtie 2 index
bowtie2-inspect-l -s ref_large

# List reference names only
bowtie2-inspect-l -n ref_large

# Recover FASTA from a large index
bowtie2-inspect-l ref_large > ref_large.fa

# Save summary output to a file
bowtie2-inspect-l -s ref_large -o ref_large.summary.txt

Recommended Workflow

1. Identify the bt2 base name (filename minus .1.bt2l or .2.bt2l extension)
2. Run bowtie2-inspect-l -s <bt2_base> to get a summary of the index
3. Use -n to list reference sequence names only, or default for FASTA output
4. Redirect output to a file with -o <filename> if needed

Guardrails

• Input must be a Bowtie 2 large index (.bt2l format), not standard .bt2
• The <bt2_base> argument excludes the trailing .1.bt2l/.2.bt2l extension
• Use bowtie2-inspect (without -l) for standard non-large indexes
• The direct executable prints a wrapper warning on startup; that is expected and not itself an error