subread-align

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

# 1) Genomic DNA-seq alignment
subread-align \
  -i ref_index \
  -r reads.fastq.gz \
  -t 1 \
  -o sample.bam \
  -T 8

# 2) Paired-end RNA-seq alignment
subread-align \
  -i ref_index \
  -r sample_R1.fastq.gz \
  -R sample_R2.fastq.gz \
  -t 0 \
  -o sample.bam \
  -T 8

# 3) Coordinate-sorted BAM ready for genome-browser loading
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

1. Build the index first with subread-buildindex and keep the basename stable.
2. Choose -t 0 for RNA-seq and -t 1 for genomic DNA before tuning anything else.
3. Add paired-end orientation and fragment constraints only if the library design requires it.
4. 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.