Bio Read Alignment Bowtie2 Alignment

What it does

When your agent uses it

• Aligning ChIP/ATAC/CUT&RUN reads
• Read ends are adapter-contaminated and need soft-clipping
• A tunable sensitivity/speed preset is wanted

Example prompts

• “Use the bio-read-alignment-bowtie2-alignment skill to align DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align)…”
• “/bio-read-alignment-bowtie2-alignment”

Requirements

• A Bash shell

Workflow steps

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

1. 1End-to-end (default) vs --local is a biology decision about whether the full read must align. End-to-end forces the entire read to match…
2. 2Bowtie2 MAPQ is a different scale from BWA and caps low. It is AS/XS-driven and discrete, capping at 42 in end-to-end mode and 44 in local…
3. 3For peak assays, the fragment-geometry flags set the coordinates the peak caller consumes. ChIP/ATAC interpret signal at the fragment…

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 Read Alignment Bowtie2 Alignment loads about 3.6k tokens when it runs. Until then it costs about 199 tokens; SKILL.md has 1,377 words of instructions outside code blocks.

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

~199

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

~3.6k

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). 1,377 words, ~3,569 tokens.

name

bio-read-alignment-bowtie2-alignment

description

Aligns DNA short reads to a reference with Bowtie2, choosing end-to-end (whole read must align) vs local (soft-clip read ends) mode and a sensitivity preset; the de-facto aligner for ChIP-seq, ATAC-seq, and CUT&RUN, where fragment-geometry flags (--no-mixed, --no-discordant, --dovetail, -X) and a tool-appropriate MAPQ filter feed the peak caller. Use when aligning ChIP/ATAC/CUT&RUN reads, when read ends are adapter-contaminated and need soft-clipping, or when a tunable sensitivity/speed preset is wanted. DNA variant calling prefers bwa-alignment; RNA spliced alignment is star-alignment/hisat2-alignment; the QC gate and cross-tool MAPQ scale are alignment-files; peak calling is chip-seq/atac-seq; bisulfite uses methylation-analysis/bismark-alignment.

tool_type

cli

primary_tool

bowtie2

bowtie2-build --threads 8 reference.fa reference_index
# emits reference_index.{1,2,3,4}.bt2 and .rev.{1,2}.bt2. Pass the BASENAME (reference_index) to -x, NOT a file.

# Paired-end, streamed to a sorted BAM. Bowtie2 prints the alignment summary to stderr.
bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz 2> align.log | \
    samtools sort -@ 4 -o aligned.sorted.bam -
samtools index aligned.sorted.bam
# single-end: -U reads.fq.gz instead of -1/-2.

bowtie2 -p 8 --very-sensitive --no-mixed --no-discordant \
    --rg-id sample1 --rg SM:sample1 --rg PL:ILLUMINA --rg LB:lib1 \
    -x reference_index -1 chip_1.fq.gz -2 chip_2.fq.gz 2> chip.log | \
    samtools view -bS -q 30 -F 1804 - | \
    samtools sort -@ 4 -o chip.bam -
# -q 30 drops multimappers (Bowtie2 scale: max 42 e2e); -F 1804 removes unmapped/secondary/dup/QC-fail.

# Local mode + dovetail + wide -X for adapter read-through and nucleosome-spanning short fragments.
bowtie2 -p 8 --very-sensitive --local --dovetail -X 2000 --no-mixed --no-discordant \
    -x reference_index -1 atac_1.fq.gz -2 atac_2.fq.gz 2> atac.log | \
    samtools view -bS -q 30 -F 1804 - | \
    samtools sort -@ 4 -o atac.bam -
# The Tn5 +4/-5 cut-site shift is a DOWNSTREAM signal-track transform, not done here -> atac-seq.

bowtie2 --very-fast       -x index -1 r1.fq -2 r2.fq    # -D 5  -R 1 -N 0 -L 22 -i S,0,2.50
bowtie2 --sensitive       -x index -1 r1.fq -2 r2.fq    # -D 15 -R 2 -N 0 -L 22 -i S,1,1.15  (DEFAULT)
bowtie2 --very-sensitive  -x index -1 r1.fq -2 r2.fq    # -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
# Append -local for the local-mode presets (e.g. --very-sensitive-local). Higher -D/-R/shorter -L = more sensitive, slower.

bowtie2 -k 5  -x index -1 r1.fq -2 r2.fq -S out.sam     # up to 5 alignments/read (MAPQ unreliable in -k)
bowtie2 -a    -x index -1 r1.fq -2 r2.fq -S out.sam     # ALL alignments (slow on repetitive genomes)
bowtie2 --un-conc-gz unmapped_%.fq.gz -x index -1 r1.fq.gz -2 r2.fq.gz -S out.sam  # save unaligned pairs

© 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 2 other files in read-alignment/bowtie2-alignment of GPTomics/bioSkills.

• SKILL.md
• examples/align_bowtie2.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-read-alignment-bowtie2-alignment