starlong-avx2

name	starlong-avx2
description	Use when aligning long RNA-seq reads to a reference genome using the AVX2-optimized STARlong aligner for splice-aware mapping.
disable-model-invocation	true
user-invocable	true

starlong-avx2

Quick Start

• Command: STARlong-avx2 --genomeDir /path/to/index --readFilesIn reads.fq
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-avx2
• Full reference: references/help.md

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 AVX2-optimized binary.

Common Patterns

# 1) Build a genome index for STARlong
STARlong-avx2 \
  --runMode genomeGenerate \
  --genomeDir starlong_index \
  --genomeFastaFiles genome.fa \
  --sjdbGTFfile genes.gtf \
  --runThreadN 16

# 2) Align long reads from FASTQ
STARlong-avx2 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq \
  --runThreadN 16

# 3) Align gzipped long reads and emit sorted BAM
STARlong-avx2 \
  --genomeDir starlong_index \
  --readFilesIn longreads.fastq.gz \
  --readFilesCommand zcat \
  --outSAMtype BAM SortedByCoordinate \
  --runThreadN 16

Recommended Workflow

1. Prepare or obtain a genome index directory using --runMode genomeGenerate with FASTA and optional GTF files
2. Run alignment with STARlong-avx2 --genomeDir <index> --readFilesIn <reads> adjusting --runThreadN for parallelism
3. Use --readFilesCommand zcat for gzipped input files as needed
4. Review output files (Aligned.out.sam, SJ.out.tab) and check Log.final.out for mapping statistics

Guardrails

• Always specify --genomeDir pointing to a valid STAR genome index directory
• Set --runThreadN appropriately for available CPU cores to avoid resource contention
• Ensure input read files match the expected format (FASTA/FASTQ); use --readFilesCommand for compressed files