subread-fullscan

name	subread-fullscan
description	Use when scanning a reference index for all high-similarity genomic locations of one specific read sequence string.
disable-model-invocation	true
user-invocable	true

subread-fullscan

Quick Start

• Command: subread-fullscan [options] -i <index_name> <read_string>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/subread-fullscan
• Reference: See references/help.md; local no-argument execution is the most useful way to see usage text

When To Use This Tool

• Use subread-fullscan when you want to probe where one literal read sequence could map across the whole indexed genome.
• It is a diagnostic or exploratory tool, not a bulk FASTQ aligner.
• Reach for it when validating whether a short sequence is repetitive, checking match specificity at a chosen identity threshold, or debugging why a read behaves oddly in the main aligner.

Common Patterns

# Scan the genome for all high-similarity hits to one read sequence
subread-fullscan -i ref_index ACGTACGTACGTACGT

# Tighten the minimum matched fraction
subread-fullscan -i ref_index -m 0.95 ACGTACGTACGTACGT

Recommended Workflow

1. Make sure the relevant Subread index already exists and note its basename.
2. Provide the query as a literal read string, not a FASTQ filename.
3. Start with the default match threshold, then increase -m if too many repetitive hits are returned.
4. Use the result as a debugging or interpretive aid before changing cohort-wide alignment settings.

Guardrails

• The final argument is a literal read sequence string. This command does not take a FASTQ or FASTA file as input.
• -i expects the index basename, not the reference FASTA.
• Local testing shows that running with no arguments prints useful usage text, while --help and --version are not real help paths.
• -m is a fraction of matched bases, not a count.