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Bio Read Alignment Bowtie2 Alignment · FreedomIntelligence | DecimalAI

Bio Read Alignment Bowtie2 Alignment

SkillScore96Maintained

bio-read-alignment-bowtie2-alignment

Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.

scienceby FreedomIntelligence

Links this skill to your agents and keeps it current with the author’s updates.

Automatic

Research pack

1 · One-time — install the CLI (docs ↗)

pip install decimalai

2 · Get the skill — writes .claude/skills/bio-read-alignment-bowtie2-alignment/SKILL.md

decimalai skills pull bio-read-alignment-bowtie2-alignment --out .claude/skills/

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/bio-read-alignment-bowtie2-alignment/SKILL.md https://app.decimal.ai/s/bio-read-alignment-bowtie2-alignment/SKILL.md

Raw file: /s/bio-read-alignment-bowtie2-alignment/SKILL.md ↗ · machine-readable summary at /s/bio-read-alignment-bowtie2-alignment.json ↗

In productionGlobal

how this skill behaves on real traffic · last 30 days

No production data for this skill yet — usage numbers appear here once agents start running it.

Anonymized aggregate across every org using this skill — proof from real production use, not a demo.

Does this skill help? · Benchmark: with vs. withoutsign in to run this on your agents

23 test cases from the publisher’s eval.yaml · each run twice on gemini-3.6-flash — with the skill injected, then without · last run 50d ago

Yes — +9% lift · at higher cost+102% tokens0% turns96% of whole cases pass with skill (22/23)

Test case	Without → With	Effect	Δ tokens	Δ turns
case-01	✗→✓	▲ Improved	42%	0%
case-05	✗→✓	▲ Improved	81%	0%
case-02	✓→✓	＝ Same ✓	69%	0%
case-11	✓→✓	＝ Same ✓	228%	0%
case-04	✓→✓	＝ Same ✓	51%	0%

Showing 5 of 23 cases

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/1/2026

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

FreedomIntelligence / OpenClaw-Medical-Skills

skills/bio-read-alignment-bowtie2-alignment/SKILL.md

View on GitHub ↗

Imported 8/1/2026Version v2

Skill contents

SKILL.md

<!--

COPYRIGHT NOTICE

This file is part of the "Universal Biomedical Skills" project.

Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>

All Rights Reserved.

This code is proprietary and confidential.

Unauthorized copying of this file, via any medium is strictly prohibited.

Provenance: Authenticated by MD BABU MIA

-->

Bowtie2 Alignment

Build Index

bash
# Build index from reference FASTA
bowtie2-build reference.fa reference_index

# With threads (faster)
bowtie2-build --threads 8 reference.fa reference_index

# Creates: reference_index.1.bt2, .2.bt2, .3.bt2, .4.bt2, .rev.1.bt2, .rev.2.bt2

Basic Alignment

bash
# Paired-end reads
bowtie2 -p 8 -x reference_index -1 reads_1.fq.gz -2 reads_2.fq.gz -S aligned.sam

# Single-end reads
bowtie2 -p 8 -x reference_index -U reads.fq.gz -S aligned.sam

# Direct to sorted BAM
bowtie2 -p 8 -x reference_index -1 r1.fq.gz -2 r2.fq.gz | \
    samtools sort -@ 4 -o aligned.sorted.bam -

Alignment Modes

bash
# End-to-end mode (default) - align entire read
bowtie2 --end-to-end -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Local mode - soft-clip ends for better alignment
bowtie2 --local -x index -1 r1.fq -2 r2.fq -S aligned.sam

Sensitivity Presets

bash
# Very fast (less sensitive)
bowtie2 --very-fast -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Fast
bowtie2 --fast -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Sensitive (default)
bowtie2 --sensitive -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Very sensitive (slower but more accurate)
bowtie2 --very-sensitive -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Local mode equivalents
bowtie2 --very-sensitive-local -x index -1 r1.fq -2 r2.fq -S aligned.sam

ChIP-seq Alignment

bash
# Typical ChIP-seq settings
bowtie2 -p 8 \
    --very-sensitive \
    --no-mixed \
    --no-discordant \
    -x index -1 chip_1.fq.gz -2 chip_2.fq.gz | \
    samtools view -bS -q 30 -F 4 - | \
    samtools sort -o chip.sorted.bam -

ATAC-seq Alignment

bash
# ATAC-seq with size selection
bowtie2 -p 8 \
    --very-sensitive \
    -X 2000 \                    # Max fragment length
    --no-mixed \
    --no-discordant \
    -x index -1 atac_1.fq.gz -2 atac_2.fq.gz | \
    samtools view -bS -q 30 - | \
    samtools sort -o atac.sorted.bam -

Fragment Size Options

bash
# Set expected insert size range
bowtie2 -p 8 \
    -I 100 \     # Minimum fragment length
    -X 500 \     # Maximum fragment length
    -x index -1 r1.fq -2 r2.fq -S aligned.sam

Read Group and Output Options

bash
# Add read group
bowtie2 -p 8 \
    --rg-id sample1 \
    --rg SM:sample1 \
    --rg PL:ILLUMINA \
    --rg LB:lib1 \
    -x index -1 r1.fq -2 r2.fq -S aligned.sam

Multi-mapping Reads

bash
# Report up to k alignments per read
bowtie2 -k 5 -x index -1 r1.fq -2 r2.fq -S aligned.sam

# Report all alignments
bowtie2 -a -x index -1 r1.fq -2 r2.fq -S aligned.sam

Output Unmapped Reads

bash
# Write unmapped reads to separate files
bowtie2 -p 8 \
    --un-conc-gz unmapped_%.fq.gz \
    -x index -1 r1.fq.gz -2 r2.fq.gz -S aligned.sam

Key Parameters

| Parameter | Default | Description | |-----------|---------|-------------| | -p | 1 | Number of threads | | -x | - | Index basename | | -1/-2 | - | Paired-end reads | | -U | - | Single-end reads | | -I | 0 | Min fragment length | | -X | 500 | Max fragment length | | -k | 1 | Report up to k alignments | | --no-mixed | off | Suppress unpaired alignments | | --no-discordant | off | Suppress discordant alignments |

Alignment Statistics

bash
# Bowtie2 prints alignment summary to stderr
bowtie2 -p 8 -x index -1 r1.fq -2 r2.fq -S aligned.sam 2> alignment_stats.txt

Example output:

1000000 reads; of these:
  1000000 (100.00%) were paired; of these:
    50000 (5.00%) aligned concordantly 0 times
    900000 (90.00%) aligned concordantly exactly 1 time
    50000 (5.00%) aligned concordantly >1 times
95.00% overall alignment rate

Related Skills

read-qc/fastp-workflow - Preprocess reads before alignment
alignment-files/alignment-sorting - Post-alignment processing
chip-seq/peak-calling - ChIP-seq analysis
atac-seq/atac-peak-calling - ATAC-seq analysis

Illustrative Want to see what bio-read-alignment-bowtie2-alignment would put in front of your model? Preview the rendered body and check its trigger phrases — no LLM call, no signup.

Latest benchmark · publisher runVerified

8/2/2026, 16:37 UTC · 23 cases

Lift

+9%

96% vs 87%

Agent turns

1.0 vs 1.0

Tokens

+102%

2,308.61 vs 1,145.74

fail → pass · 2pass → pass · 20fail → fail · 1

Per-case results (23)

Case	Status	Duration (ms)			Turns			Tokens			Tool calls
Case	Status	Without	With	Δ	Without	With	Δ	Without	With	Δ	Without	With	Δ
case-01 I have paired-end RNA-seq FASTQ files from a mammalian sample and need to perform splice-aware alignment across genomic introns to quantify gene expression. How should I perform this alignment?	fail→pass	14,099	11,578	-18%	1	1	0%	2,614	3,703	+42%	0	0	—
case-02 I need a command to filter low-quality reads and cut Illumina adapter sequences from raw FASTQ files before running any aligner.	pass→pass	8,912	7,712	-13%	1	1	0%	1,824	3,079	+69%	0	0	—
case-11 Which preset flag should be used when running Bowtie2 in local mode with maximum sensitivity settings?	pass→pass	3,463	2,505	-28%	1	1	0%	569	1,869	+228%	0	0	—
case-03 Given a sorted BAM file resulting from a sequencing run, what command should I run to mark PCR duplicates prior to peak calling?	fail→fail	13,039	5,221	-60%	1	1	0%	1,764	2,516	+43%	0	0	—
case-04 I have paired-end ATAC-seq reads (`sample_R1.fastq.gz` and `sample_R2.fastq.gz`) and need a bash command to align them against my genome index `hg38_index`. Can you write a command pipeline that runs Bowtie2 with settings tailored for ATAC-seq data and outputs directly into a sorted BAM file named `sample_sorted.bam`?	pass→pass	8,987	5,122	-43%	1	1	0%	1,755	2,648	+51%	0	0	—
case-05 Please provide a single bash pipeline command to align my paired-end ChIP-seq reads (`chip_1.fq.gz`, `chip_2.fq.gz`) using Bowtie2 and the index `ref_idx`. The pipeline should pipe the alignment into samtools to filter for high quality aligned pairs and output a final sorted BAM file.	fail→pass	7,722	5,017	-35%	1	1	0%	1,464	2,649	+81%	0	0	—
case-06 Write a bash command to build a Bowtie2 reference index named `mm10_idx` from a genome fasta file `mm10.fa` using 8 parallel processing threads.	pass→pass	2,756	1,885	-32%	1	1	0%	485	1,839	+279%	0	0	—
case-07 I need a one-line bash command pipeline to align paired FASTQ files `reads_1.fq.gz` and `reads_2.fq.gz` against reference index `hg38` using 8 threads and write directly to a sorted BAM file `aligned.sorted.bam`.	pass→pass	4,853	3,975	-18%	1	1	0%	917	2,339	+155%	0	0	—
case-08 How do I align a single-end gzipped FASTQ file `se_reads.fq.gz` using Bowtie2 against index `tair10` with 4 threads, saving output to `se_aligned.sam`?	pass→pass	2,946	2,623	-11%	1	1	0%	565	2,090	+270%	0	0	—
case-09 My sequencing reads contain poor-quality vector sequences at the 3' and 5' ends that prevent full-length end-to-end alignment. What parameter should I add to Bowtie2 to allow soft-clipping of read ends?	pass→pass	7,190	4,131	-43%	1	1	0%	1,266	2,307	+82%	0	0	—
case-10 I am willing to sacrifice computational speed to achieve the highest possible alignment accuracy and sensitivity for my reads. Which Bowtie2 preset option should I use?	pass→pass	10,626	4,384	-59%	1	1	0%	1,483	2,275	+53%	0	0	—
case-12 I have a paired-end library with an expected insert size between 100 bp and 600 bp. Which Bowtie2 parameters should I set to restrict the minimum and maximum valid fragment lengths?	pass→pass	6,322	2,991	-53%	1	1	0%	1,255	2,080	+66%	0	0	—
case-13 I need to add read group headers during Bowtie2 alignment for sample 'NA12878', library 'lib1', platform 'ILLUMINA', and read group ID 'rg1'. What flags should be added to the bowtie2 invocation?	pass→pass	4,391	3,554	-19%	1	1	0%	926	2,329	+152%	0	0	—
case-14 I want Bowtie2 to report up to 10 valid alignment locations for each read instead of picking just the top single alignment. What command flag controls this?	pass→pass	3,077	2,486	-19%	1	1	0%	511	1,982	+288%	0	0	—
case-15 Which Bowtie2 option instructs the aligner to search for and report all possible alignments across the reference genome for each read?	pass→pass	4,086	3,589	-12%	1	1	0%	662	1,934	+192%	0	0	—
case-16 I want to capture paired-end reads that failed to align into separate compressed FASTQ files named `unmapped_1.fq.gz` and `unmapped_2.fq.gz`. Which Bowtie2 parameter handles this?	pass→pass	6,331	2,661	-58%	1	1	0%	1,294	2,079	+61%	0	0	—
case-17 Bowtie2 prints alignment summary metrics to standard error. How can I redirect these summary statistics into a text file `alignment_summary.txt` while keeping the SAM output standard?	pass→pass	8,164	5,371	-34%	1	1	0%	1,529	2,493	+63%	0	0	—
case-18 When aligning paired-end reads, I want to strictly prevent Bowtie2 from trying to align individual reads as singletons if the pair fails to align together. What parameter enforces this?	pass→pass	4,860	3,883	-20%	1	1	0%	843	2,280	+170%	0	0	—
case-19 I want Bowtie2 to align paired-end reads only when both reads align with valid orientation and distance, suppressing any discordant pairs. Which option accomplishes this?	pass→pass	7,227	3,799	-47%	1	1	0%	1,261	2,173	+72%	0	0	—
case-20 I need to perform a fast initial alignment test on a subset of reads where processing speed is prioritized over maximum sensitivity. Which preset option should be passed?	pass→pass	6,397	2,996	-53%	1	1	0%	1,076	2,065	+92%	0	0	—
case-21 In a pipeline piping Bowtie2 SAM output into samtools view, which samtools filter flag removes unmapped reads from the output stream?	pass→pass	5,107	4,061	-20%	1	1	0%	848	2,252	+166%	0	0	—
case-22 What flag is used to instruct Bowtie2 to use 16 CPU cores for parallel alignment calculation?	pass→pass	7,190	1,939	-73%	1	1	0%	342	1,843	+439%	0	0	—
case-23 When `bowtie2-build genome.fa human_index` completes successfully, what file extension patterns are generated for a standard Bowtie2 index?	pass→pass	5,396	3,627	-33%	1	1	0%	1,099	2,274	+107%	0	0	—

These cases were also screened by the skill’s intent / safety pass.See the Trust review ↗Reproduce this benchmark in Colab ↗

How this skill was measured

DecimalAI ran this skill against gemini-3.6-flash twice over the same eval suite — once with the skill loaded and once without — and compared the two runs case by case. 23 cases were attempted. The headline lift of +9 percentage points is the difference between those two pass rates over the 23 comparable cases.

Model measured: gemini-3.6-flash
Graded by: gemini-3.6-flash
Grading method: judged
Verification: verified
Pass rate without the skill: 87%
Pass rate with the skill: 95.7%
Cases attempted: 23
Cases counted toward lift: 23
Cases that regressed: 0
Skill version measured: v2
Run completed: 8/2/2026, 16:37 UTC

Measured example — same prompt, with vs. without the skill · from the benchmark run · case case-01

Prompt

I have paired-end RNA-seq FASTQ files from a mammalian sample and need to perform splice-aware alignment across genomic introns to quantify gene expression. How should I perform this alignment?

Without the skill loaded, the model failed this case. With it loaded, the same prompt on the same model passed. This is one improved case from the latest verified run; every case, including any that regressed, is in the table above.

Show both answers

SkillScore blends 4 signals1 of 4 complete

BenchmarkPass rate WITH skill on a verified run96

Live evalNeeds ≥10 evaluated traces in 30 days

AI ratingNeeds ≥10 rated traces

AdoptionNeeds ≥10 serves across ≥2 orgs in 30 days

Efficiency · separate axis (at equal correctness)+0% turns+116% tokens

Shown for transparency; not credited unless a verified run shows no correctness regression.

Backed by 1 of 4 signals — each added signal makes the score more robust.

Verified on gemini-3.6-flash · re-tested 49 days ago

Model	Method	Date	Lift
gemini-3.6-flash	verified	7/26/2026	0%

Other measured skills in the registry, with their headline benchmark lift.