starlong-avx

name	starlong-avx
description	Use when aligning long RNA-seq reads to a reference genome with splice-aware mapping, or when generating STAR genome indices for long-read data.
disable-model-invocation	true
user-invocable	true

starlong-avx

Quick Start

• Command: STARlong-avx
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/STARlong-avx
• Full reference: See references/help.md for complete options and parameters

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 AVX-optimized binary.

Common Patterns

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

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

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

Recommended Workflow

1. Prepare reference genome FASTA and optional GTF annotation file
2. Generate genome index: STARlong-avx --runMode genomeGenerate --genomeDir <index_dir> --genomeFastaFiles <genome.fa> --sjdbGTFfile <annot.gtf> --runThreadN <threads>
3. Align long reads: STARlong-avx --genomeDir <index_dir> --readFilesIn <reads.fq> --runThreadN <threads>
4. Review output alignments (SAM/BAM) and splice junction files (SJ.out.tab)

Guardrails

• Always specify --genomeDir pointing to a valid STAR genome index directory
• Ensure --runThreadN matches available CPU cores to avoid resource contention
• Use --readFilesCommand zcat for gzipped input files; STAR expects uncompressed FASTA/FASTQ by default