Our review
Aligns long FASTQ reads (PacBio, Oxford Nanopore) to a reference genome using Subread's long-read aligner, optionally in RNA-seq mode.
Strengths
- Optimized for long sequencing reads
- Supports RNA-seq mode with the -X flag
- Outputs BAM or SAM files suitable for downstream analysis
Limitations
- Requires a full single-block Subread index
- Input format limited to FASTQ (or gzipped)
- The -h flag does not display help correctly
Use sublong when you need to align long reads (PacBio, ONT) to a reference genome and produce BAM or SAM output.
Avoid sublong if your reads are short or if you have a multi-block index, as it is not designed for those scenarios.
Security analysis
SafeThe skill only documents safe, standard bioinformatics commands (sublong alignment). No destructive actions, data exfiltration, or obfuscated payloads. The tool is a local executable, and usage is limited to alignment tasks.
No concerns found
Examples
Align the long reads in long_reads.fastq.gz to the index named long_index using sublong with 8 threads, outputting BAM to aligned.bam.Run sublong in RNA-seq mode (-X) to align isoform reads from isoform_reads.fastq.gz against the transcriptome index transcriptome_index, output BAM to isoforms.bam with 8 threads.Align long_reads.fastq.gz to index long_index using sublong and output in SAM format (not BAM) to aligned.sam.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
-Xflag
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
- Build a full one-block Subread index first, usually via
subread-buildindex -F -B. - Prepare long reads in FASTQ or gzipped FASTQ format.
- Decide whether you want standard genomic alignment or RNA-seq mode with
-X. - Run
sublongwith an explicit output file and thread count. - 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
--SAMoutputexplicitly if SAM format is required -his not a true help switch here. Local testing shows--helpand--versionboth print usage text and then complain about the unrecognized option;-vis the real version flag.-ois mandatory forsublong; unlike some other Subread tools, output is not optional.-Xswitches on RNA-seq mode but does not replace the need for an index compatible with the same reference build you expect downstream.
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