sublong

name	sublong
description	Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
disable-model-invocation	true
user-invocable	true

sublong

Quick Start

• Command: sublong -i <index_name> -r <input.fastq> -o <output.bam>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/sublong
• Full reference: See references/help.md

When To Use This Tool

• Aligning long reads (e.g., PacBio, Oxford Nanopore) to a reference genome
• Mapping reads against a full Subread index with a single block
• Producing BAM or SAM output for downstream analysis
• RNA-seq mode alignment via the -X flag

Common Patterns

# Align long genomic reads and write BAM output
sublong -i long_index -r long_reads.fastq.gz -o long_reads.bam -T 8

# Run in long-read RNA-seq mode
sublong -i transcriptome_index -r isoform_reads.fastq.gz -o isoform_reads.bam -X -T 8

# Emit SAM instead of BAM
sublong -i long_index -r long_reads.fastq.gz -o long_reads.sam --SAMoutput

Recommended Workflow

1. Build a full one-block Subread index first, usually via subread-buildindex -F -B.
2. Prepare long reads in FASTQ or gzipped FASTQ format.
3. Decide whether you want standard genomic alignment or RNA-seq mode with -X.
4. Run sublong with an explicit output file and thread count.
5. Validate the BAM or SAM output before downstream quantification, QC, or variant analysis.

Guardrails

• The index must be a full index with exactly one block; multi-block indexes are not supported
• Input must be FASTQ or gzipped FASTQ; other formats are not accepted
• Default output is BAM; use --SAMoutput explicitly if SAM format is required
• -h is not a true help switch here. Local testing shows --help and --version both print usage text and then complain about the unrecognized option; -v is the real version flag.
• -o is mandatory for sublong; unlike some other Subread tools, output is not optional.
• -X switches on RNA-seq mode but does not replace the need for an index compatible with the same reference build you expect downstream.