starlong-sse4-1

name	starlong-sse4-1
description	Use when aligning long RNA-seq reads to a reference genome or generating genome indexes for spliced transcript alignment
disable-model-invocation	true
user-invocable	true

starlong-sse4-1

Quick Start

• Command: STARlong-sse4.1
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-sse4.1
• Full reference: See references/help.md for complete parameter documentation

When To Use This Tool

• Align long RNA-seq reads from PacBio or Nanopore with STARlong.
• Build or reuse STAR-compatible genome indices for long-read splice-aware mapping.
• Map full-length transcript reads while keeping STAR-style splice-junction outputs.
• Run a long-read-focused STAR wrapper using the SSE4.1-optimized binary.

Common Patterns

# 1) Build a genome index for STARlong
STARlong-sse4.1 \
  --runMode genomeGenerate \
  --genomeDir starlong_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align long reads from FASTQ
STARlong-sse4.1 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# 3) Align gzipped long reads and emit sorted BAM
STARlong-sse4.1 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Generate a genome index: STARlong-sse4.1 --runMode genomeGenerate --genomeDir /path/to/index --genomeFastaFiles ref.fa --sjdbGTFfile annotations.gtf
2. Prepare long-read input files in FASTA/FASTQ format
3. Align reads: STARlong-sse4.1 --genomeDir /path/to/index --readFilesIn reads.fq --runThreadN N
4. Review output alignments (SAM/BAM) and splice junction files (SJ.out.tab)

Guardrails

• Always generate or obtain a compatible genome index before running alignment
• Scale --genomeSAindexNbases down for small genomes (min(14, log2(GenomeLength)/2 - 1))
• Ensure input format matches --readFilesType (default Fastx for FASTA/FASTQ)