starlong

name	starlong
description	Use when aligning long RNA-seq reads with STARlong through the CPU-dispatch wrapper installed in this environment.
disable-model-invocation	true
user-invocable	true

starlong

Shell wrapper around multiple STARlong-* binaries. It chooses the best SIMD build available for the current CPU (avx2, avx, sse4.1, ssse3, sse3, sse2, sse) and otherwise falls back to STARlong-plain, while exposing the normal STARlong command-line interface.

Quick Start

• Command: STARlong --genomeDir /path/to/index --readFilesIn reads.fastq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong
• Observed version: 2.7.11b

When To Use This Tool

• Aligning PacBio or Nanopore-style long RNA-seq reads with STARlong
• Using the wrapper that auto-selects a CPU-specific STARlong binary on this machine
• Building or reusing STAR-compatible genome indices for long-read splice-aware alignment
• Producing standard STAR outputs such as SAM/BAM, SJ.out.tab, and log files

Common Patterns

# Build a genome index
STARlong \
  --runMode genomeGenerate \
  --genomeDir starlong_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# Align long reads
STARlong \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# Align gzipped reads and emit coordinate-sorted BAM
STARlong \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Generate a compatible STAR genome index, optionally with --sjdbGTFfile for splice annotations.
2. Run the STARlong wrapper rather than hard-coding one SIMD binary unless you specifically need a fixed backend.
3. Add --readFilesCommand zcat or a similar decompressor for compressed inputs.
4. Review the standard STAR outputs along with long-read-specific alignment quality and splice-junction summaries.

Guardrails

• STARlong is a wrapper script, not the aligner binary itself. bash -x STARlong --version on this host showed it selecting STARlong-avx2.
• --help shows the generic STAR usage banner (Usage: STAR ...) because the wrapper forwards directly to the selected backend.
• --version works and returned 2.7.11b locally.
• Help text declares versionGenome 2.7.4a as the earliest compatible genome index version for this release.
• Genome FASTA files for --runMode genomeGenerate must be plain text and cannot be zipped.
• Default output is SAM (outSAMtype SAM), so request BAM explicitly when needed.
• Help text exposes STARlong-specific window coverage controls such as winReadCoverageRelativeMin and winReadCoverageBasesMin; adjust them only if you intentionally tune long-read sensitivity.