Bio Long Read Sequencing Long Read Alignment

What it does

When your agent uses it

• Choosing a minimap2 preset by platform/chemistry
• Preparing input for Clair3/medaka/Sniffles/modkit
• Aligning into repeats/centromeres
• Spliced-aligning cDNA/Iso-Seq

Example prompts

• “Use the bio-long-read-sequencing-long-read-alignment skill to align Oxford Nanopore and PacBio long reads (and assemblies) to a reference with…”
• “/bio-long-read-sequencing-long-read-alignment”

Requirements

• A Bash shell

Workflow steps

3 steps, taken from the first numbered list in SKILL.md.

1. 1Preset = read error rate, not platform. "ONT" is no longer one regime: noisy R9/fast/hac = map-ont; accurate Q20+/duplex/R10-sup = lr:hq…
2. 2Supplementary alignments ARE the SV signal. SV callers read the split-read pattern (primary + supplementary chimeric pieces), not the tidy…
3. 3A tag absent at alignment time is unrecoverable. MM/ML, MD, cs - if minimap2 did not write them, no downstream tool can reconstruct them…

What it can do on your machine

Read from SKILL.md and the folder at commit d91ed3d. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships script files (Shell), which the agent can run.

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  No URLs in SKILL.md.

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names no API keys, tokens, secrets or passwords.

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Bio Long Read Sequencing Long Read Alignment loads about 3.3k tokens when it runs. Until then it costs about 196 tokens; SKILL.md has 1,350 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~196

When it runs · the whole SKILL.md, loaded when a task matches

~3.3k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from GPTomics/bioSkills at commit d91ed3d, republished under its MIT licence (© GPTomics). 1,350 words, ~3,314 tokens.

name

bio-long-read-sequencing-long-read-alignment

description

Aligns Oxford Nanopore and PacBio long reads (and assemblies) to a reference with minimap2 using the error-rate-matched preset (map-ont, lr:hq, map-hifi, map-pb, splice/splice:hq, asm5/10/20, ava), producing a sorted/indexed BAM for variant, SV, methylation, or isoform analysis. Covers why the preset rewrites the scoring/chaining model, why SV calling rides on supplementary not secondary alignments, carrying MM/ML methylation tags through with -y, the multi-part-index MAPQ trap, and when to swap in Winnowmap/VACmap/lra/pbmm2. Use when mapping ONT or PacBio reads, choosing a minimap2 preset by platform/chemistry, preparing input for Clair3/medaka/Sniffles/modkit, aligning into repeats/centromeres, or spliced-aligning cDNA/Iso-Seq.

tool_type

cli

primary_tool

minimap2

# Accurate ONT (Q20+/R10 sup) -> genome, SV+variant ready, sorted+indexed
minimap2 -ax lr:hq -t 16 --MD -Y -R '@RG\tID:s1\tSM:s1' ref.fa reads.fq.gz \
  | samtools sort -@4 -o aln.bam && samtools index aln.bam

# Noisy ONT (R9 / fast / hac)
minimap2 -ax map-ont -t 16 --MD -Y ref.fa r9.fq.gz | samtools sort -o ont.bam

# PacBio HiFi (minimap2, or pbmm2 in one sorted+indexed call)
minimap2 -ax map-hifi -t 16 --MD -Y ref.fa hifi.fq.gz | samtools sort -o hifi.bam
pbmm2 align --preset HIFI --sort -j 16 ref.fa hifi.bam hifi.aligned.bam

# Methylation passthrough: carry Dorado MM/ML through alignment (the -y trap). -Y soft-clips
# supplementary records so hard-clipping does not break the MM per-base skip counting.
samtools fastq -T MM,ML dorado.mod.bam \
  | minimap2 -ax lr:hq -y -Y --MD ref.fa - \
  | samtools sort -o meth.bam        # then modkit pileup meth.bam ...

# Direct RNA (ONT): stranded forward-only, small k for terminal-exon sensitivity
minimap2 -ax splice -uf -k14 -G500k ref.fa dRNA.fq.gz | samtools sort -o drna.bam
#   -G500k raises max-intron above the 200k default only for genes with long introns

# Assembly-to-reference: PAF is correct here; --cs enables paftools variant calling
minimap2 -cx asm5 --cs ref.fa asm.fa > asm.paf
paftools.js call asm.paf > asm.var.vcf

# Repeats / centromeres / T2T: Winnowmap (precompute repetitive k-mers)
meryl count k=15 output merylDB ref.fa
meryl print greater-than distinct=0.9998 merylDB > repetitive_k15.txt
winnowmap -W repetitive_k15.txt -ax map-ont ref.fa reads.fq.gz | samtools sort -o wm.bam

# Prebuild index - bake the SAME preset's k/w in (else the preset's k/w is ignored)
minimap2 -x lr:hq -d ref.lrhq.mmi ref.fa

© GPTomics, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 3 other files in long-read-sequencing/long-read-alignment of GPTomics/bioSkills.

• SKILL.md
• examples/methylation_passthrough.sh
• examples/minimap2_align.sh
• usage-guide.md

Open the folder on GitHubat commit d91ed3d

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in GPTomics/bioSkills, which our catalogue first saw on October 7, 2026.

• PKU-YuanGroup/OpenAI4Sskills/bioskills/bio-long-read-sequencing-long-read-alignment