| name | subread-align |
| description | Use when aligning RNA-seq or genomic DNA-seq reads to a reference index. Supports paired-end and single-end reads in FASTQ, FASTA, SAM, or BAM formats. |
| disable-model-invocation | true |
| user-invocable | true |
subread-align
Quick Start
- Command:
subread-align -i <index_name> -r <input> -t <type> -o <output>
- Local executable:
/home/vimalinx/miniforge3/envs/bio/bin/subread-align
- Version: 2.1.1
- Full reference: See references/help.md for complete options and flags
When To Use This Tool
- Align genomic DNA-seq reads with a fast Subread-based aligner.
- Align RNA-seq reads when full splice-junction discovery is not the main requirement.
- Produce BAM output directly for downstream QC or counting.
- Prefer
subjunc instead when exon-exon junction detection is central.
Common Patterns
subread-align \
-i ref_index \
-r reads.fastq.gz \
-t 1 \
-o sample.bam \
-T 8
subread-align \
-i ref_index \
-r sample_R1.fastq.gz \
-R sample_R2.fastq.gz \
-t 0 \
-o sample.bam \
-T 8
subread-align \
-i ref_index \
-r sample_R1.fastq.gz \
-R sample_R2.fastq.gz \
-t 1 \
-o sample.bam \
-T 8 \
--sortReadsByCoordinates
Recommended Workflow
- Build the index first with
subread-buildindex and keep the basename stable.
- Choose
-t 0 for RNA-seq and -t 1 for genomic DNA before tuning anything else.
- Add paired-end orientation and fragment constraints only if the library design requires it.
- Validate mapping quality and BAM size before counting or variant calling.
Guardrails
-i, -r, and -t are mandatory, and -i expects the index basename, not the FASTA file.- Gzipped FASTQ/FASTA are auto-detected; use
--SAMinput or --BAMinput only for alignment-file input.
- Default output is BAM; use
--SAMoutput only if plain-text SAM is actually needed.
--multiMapping changes reporting behavior substantially; pair it with -B intentionally.-m, -p, -M, and -I affect sensitivity and specificity, so keep those settings cohort-consistent.
