| name | blast2sam-pl |
| description | Use when converting legacy plain-text blastn output into SAM records for downstream SAM/BAM-compatible tooling. |
| disable-model-invocation | true |
| user-invocable | true |
blast2sam-pl
Quick Start
- Command:
blast2sam.pl [-s] [-d] input.blast > output.sam
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/blast2sam.pl
- Full reference: See references/help.md
When To Use This Tool
- Convert legacy default-format
blastn text output into SAM records.
- Bridge older BLAST workflows into
samtools or other SAM/BAM-aware tooling.
- Emit aligned query sequence with
-s when downstream tools need SAM field 10 populated.
- Emit dummy quality scores with
-d when a downstream parser insists on SAM field 11.
Common Patterns
blast2sam.pl \
alignments.blast > alignments.sam
blast2sam.pl \
-sd \
alignments.blast > alignments.with-seq.sam
blast2sam.pl -sd alignments.blast > alignments.sam
samtools view -hT reference.fa alignments.sam > alignments.with-header.sam
Recommended Workflow
- Generate legacy
blastn output in the default pairwise text format, not tabular or XML output.
- Convert it with
blast2sam.pl, adding -s if downstream tools need sequence and -d if they also need quality strings.
- Add a SAM header separately if the next tool expects one.
- Inspect a few records before batch conversion, especially strand flag, position, CIGAR, and sequence fields.
Guardrails
- This parser is tailored to legacy plain-text
blastn output; it is not the right tool for BLAST tabular, XML, JSON, or generic BLAST+ -outfmt outputs.
--help works via Perl Getopt::Std, but -help is wrong here and is split into -h -e -l -p, which produces unknown-option errors.-s prints the aligned query sequence, not necessarily the original full read sequence from FASTQ input.-d fills SAM field 11 with dummy I characters (Phred 40 style); use that only when fake quality scores are acceptable.- Output is headerless and queries without alignments are omitted rather than emitted as unmapped SAM records.
