Automated summary

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

When to use it

Use sublong when you need to align long reads (PacBio, ONT) to a reference genome and produce BAM or SAM output.

When not to use it

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

Safe

Quality score90/100

The 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

How this analysis is made

Examples

Basic long-read alignment

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.

RNA-seq mode alignment

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.

SAM output format

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

Name: sublong: Long Read Aligner
Author: Skills Guide Bot

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

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 sublong with 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 --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.

From the file to a first result

The download contains exactly the content displayed on this page. This copy may differ from the latest version in the source repository.

View the source and supporting files

This download contains SKILL.md only. Any scripts, references, templates and dependencies are not included. Get the required files from the source, preserving their directory structure, before continuing.

1. Download the file

Download SKILL.md

From the root of a test project, save the file as .skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md, or use the command below. This folder is for inspecting the skill before installation.

Command for macOS/Linux or WSL: requires a POSIX shell and curl. On Windows without WSL, use the download button and create the folder manually.

mkdir -p '.skill-downloads/sublong-long-read-aligner-mrwak9j2' && curl --fail --show-error --location 'https://skills-guides.com/api/skills/sublong-long-read-aligner-mrwak9j2/download' --output '.skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md.part' && mv '.skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md.part' '.skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md'

2. Check prerequisites

Read SKILL.md before using it. If it references scripts or external services, inspect them and prepare the required access in your test environment.

No recognized prerequisites section in this file. This does not mean it is self-contained: libraries, tools and access requirements may be mentioned elsewhere in the content or source repository.

The platforms on this page are catalog indications. The paths below follow tool documentation; they do not prove this skill has been run in those tools. No minimum tool version is confirmed for this listing.

3. Load the skill

After inspection, copy the complete folder into your project using one of the commands below, then open a new tool session. The command stops if a folder with the same name already exists: compare the files before replacing it.

Claude Code

test -f '.skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md' && test -s '.skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md' && mkdir -p '.claude/skills' && test ! -e '.claude/skills/sublong' && cp -R '.skill-downloads/sublong-long-read-aligner-mrwak9j2' '.claude/skills/sublong'

OpenSkills

OpenSkills must already be installed. The local install/read procedure is checked with OpenSkills 1.5.0, which requires Node.js ≥ 20.6.0. Catalog slugs are not resolved automatically.

Official OpenSkills installation

openskills install './.skill-downloads/sublong-long-read-aligner-mrwak9j2'

openskills read 'sublong-long-read-aligner-mrwak9j2'

Reading should display the installed file content and its base directory. It does not run the skill or install its dependencies.

For an agent that reads AGENTS.md, then sync the index. This command changes AGENTS.md: review the diff before using it.

openskills sync

Manual method or another tool: attach SKILL.md to a conversation, or open it in an agent that can read files. Include any required supporting resources. No universal folder is recognized by every tool.

4. Try a first task

Use a short, synthetic input: an API endpoint, a small document or an interface brief. In a new conversation, attach the file or give the agent its path, then adapt this request:

Read .skill-downloads/sublong-long-read-aligner-mrwak9j2/SKILL.md and apply its instructions to this example: [describe a test input]. Identify any missing files, dependencies or access. Produce the result requested by the skill without inventing data or running unreviewed scripts.

Expected result: output matching the skill instructions, or a precise list of missing prerequisites. A read confirmation alone does not validate a first use. If an external resource is unavailable, that path remains untested.

Related skills

Create Interactive Maps with kepler.gl

Data & AI

Create interactive map visualizations and export standalone HTML using the keplergl Python package. Use to plot geospatial data from DataFrames, GeoJSON, or CSV.

Claude CodeCursorCodexintermediateSafe 11,995

Skills Guide Bot