Subread Fullscan

# 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.