starlong-sse3

name	starlong-sse3
description	Use when aligning long RNA-seq reads to a reference genome using STARlong with SSE3 optimization, or when generating genome indices for long-read splice-aware alignment.
disable-model-invocation	true
user-invocable	true

starlong-sse3

Quick Start

• Command: STARlong-sse3
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-sse3
• Version: 2.7.11b
• Full reference: See references/help.md for complete options

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 SSE3-optimized binary.

Common Patterns

# 1) Build a genome index for STARlong
STARlong-sse3 \
  --runMode genomeGenerate \
  --genomeDir starlong_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align long reads from FASTQ
STARlong-sse3 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# 3) Align gzipped long reads and emit sorted BAM
STARlong-sse3 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Prepare a genome directory and FASTA reference; optionally provide a GTF file with --sjdbGTFfile for splice junction annotation.
2. Generate the genome index with --runMode genomeGenerate --genomeDir <dir> --genomeFastaFiles <fasta>.
3. Align long reads with --runMode alignReads --genomeDir <dir> --readFilesIn <reads.fq>.
4. Verify output files (alignments and splice junctions) and review summary statistics before downstream analysis.

Guardrails

• Always specify --genomeDir pointing to a valid STAR genome index directory.
• Use --runThreadN to match available CPU cores; avoid oversubscribing system resources.
• For long reads, ensure the genome index was built with appropriate --genomeSAindexNbases scaled to genome size.