starlong-ssse3

name	starlong-ssse3
description	Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping using the SSSE3-optimized STARlong binary.
disable-model-invocation	true
user-invocable	true

starlong-ssse3

Quick Start

• Command: STARlong-ssse3 --genomeDir /path/to/index --readFilesIn reads.fq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-ssse3
• 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 SSSE3-optimized binary.

Common Patterns

# 1) Build a genome index for STARlong
STARlong-ssse3 \
  --runMode genomeGenerate \
  --genomeDir starlong_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align long reads from FASTQ
STARlong-ssse3 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# 3) Align gzipped long reads and emit sorted BAM
STARlong-ssse3 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Generate or obtain a genome index using --runMode genomeGenerate with FASTA and optional GTF files
2. Run alignment with STARlong-ssse3 --genomeDir /path/to/index --readFilesIn reads.fq
3. Specify thread count with --runThreadN to parallelize alignment
4. Collect output alignments (SAM/BAM) and splice junction files (SJ.out.tab)

Guardrails

• Ensure genome index compatibility; this version requires genome index version 2.7.4a or later
• Specify --readFilesCommand zcat (or similar) when input files are compressed
• Do not mix STARlong with standard STAR genome indexes; regenerate indexes appropriate for long-read mode