Bio Read Alignment Bowtie2 Alignment Agent Skill
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.
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill bio-read-alignment-bowtie2-alignmentWhat comes with it
3 357 bytes besides the instructionThe instruction itself
15 sections, as written by the authorVersion Compatibility
Reference examples tested with: samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.
Bowtie2 Alignment
"Align DNA reads with Bowtie2" → Map short reads to a reference genome using Bowtie2's end-to-end or local alignment modes.
- CLI:
bowtie2 -x index -1 R1.fq -2 R2.fq | samtools sort -o aligned.bam
Build Index
# 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
# 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
# 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
# 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
# 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
# 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
# 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
# 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
# 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
# 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
# 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
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How to use it
Take biotender-max/bio-read-alignment-bowtie2-alignment from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
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same name cannot sit side by side — one of them will be ignored.