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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.
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Install and run the BD Rhapsody™ Sequence Analysis Pipeline (v3.0) on a shared cluster or remote Linux server with no root and no container runtime. Covers the self-contained install bundle, reference archives, FASTQ manifests, per-library YML generation, SLURM array execution, outputs, sample-tag demultiplexing, and the failure modes that cost hours — wrong Sample_Tags_Version on nuclei runs, uncapped Maximum_Threads, node-local scratch, and pinning a stale `latest` bundle.
Advanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat, scvi-tools. Includes workflows for MPN, hematologic malignancies, megakaryocyte biology.
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
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| name | read-alignment-bowtie2-alignment |
| description | 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. |
| tool_type | cli |
| primary_tool | bowtie2 |
Reference examples tested with: samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
<tool> --version then <tool> --help to confirm flagsIf code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
"Align DNA reads with Bowtie2" -> Map short reads to a reference genome using Bowtie2's end-to-end or local alignment modes.
bowtie2 -x index -1 R1.fq -2 R2.fq | samtools sort -o aligned.bam# 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
# 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 -
# 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
# 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
# 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 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 -
# 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
# 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
# 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
# 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
| 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 |
# 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