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Community / AGENT SKILL
sublong
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Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.
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The full skill.
Original instructions from the publisher’s SKILL.md
# 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 ```bash # Align long genomic reads and write BAM output sublong -i long_index -r long_reads.fastq.gz -o long_reads.bam -T 8 ``` ```bash # Run in long-read RNA-seq mode sublong -i transcriptome_index -r isoform_reads.fastq.gz -o isoform_reads.bam -X -T 8 ``` ```bash # 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.