Bio Read Alignment Bwa Alignment
- 3 installs
- 1.1k repo stars
- Updated July 25, 2026
- gptomics/bioskills
Align DNA short reads to a reference genome using bwa-mem2 with read-group tags for downstream GATK.
About
Aligns DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Developers use it to align DNA short reads and produce read-group-tagged, sorted BAM files.
- bwa-mem2 index and paired/single-end alignment
- Read-group tagging for GATK-ready output
Bio Read Alignment Bwa Alignment by the numbers
- 3 all-time installs (skills.sh)
- Ranked #1,661 of 2,064 Data Science & ML skills by installs in the Skillselion catalog
- Data as of Aug 5, 2026 (Skillselion catalog sync)
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| Installs | 3 |
|---|---|
| repo stars | ★ 1.1k |
| Last updated | July 25, 2026 |
| Repository | gptomics/bioskills ↗ |
What it does
Align DNA short reads to a reference genome using bwa-mem2 with read-group tags for downstream GATK.
Files
BWA-MEM2 Alignment
Build Index
# Index reference genome (required once)
bwa-mem2 index reference.fa
# Creates: reference.fa.0123, reference.fa.amb, reference.fa.ann, reference.fa.bwt.2bit.64, reference.fa.pacBasic Alignment
# Paired-end reads
bwa-mem2 mem -t 8 reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam
# Single-end reads
bwa-mem2 mem -t 8 reference.fa reads.fq.gz > aligned.samAlignment with Read Groups
# Add read group information (required for GATK)
bwa-mem2 mem -t 8 \
-R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA\tLB:lib1' \
reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.samDirect to Sorted BAM
# Pipe to samtools for sorted BAM output
bwa-mem2 mem -t 8 \
-R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA' \
reference.fa reads_1.fq.gz reads_2.fq.gz | \
samtools sort -@ 4 -o aligned.sorted.bam -
# Index the BAM
samtools index aligned.sorted.bamMark Duplicates Pipeline
# Full pipeline: align, fixmate, sort, markdup
bwa-mem2 mem -t 8 -R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA' \
reference.fa reads_1.fq.gz reads_2.fq.gz | \
samtools fixmate -m -@ 4 - - | \
samtools sort -@ 4 - | \
samtools markdup -@ 4 - aligned.markdup.bam
samtools index aligned.markdup.bamCommon Options
bwa-mem2 mem -t 8 \ # Threads
-M \ # Mark shorter split hits as secondary (Picard compatible)
-Y \ # Use soft clipping for supplementary alignments
-K 100000000 \ # Process INT input bases in each batch
-R '@RG\tID:s1\tSM:s1' \ # Read group
reference.fa r1.fq r2.fqKey Parameters
| Parameter | Default | Description |
|---|---|---|
| -t | 1 | Number of threads |
| -k | 19 | Minimum seed length |
| -w | 100 | Band width for extension |
| -r | 1.5 | Re-seeding trigger ratio |
| -c | 500 | Skip seeds with more than INT hits |
| -A | 1 | Match score |
| -B | 4 | Mismatch penalty |
| -O | 6 | Gap open penalty |
| -E | 1 | Gap extension penalty |
| -M | off | Mark secondary alignments |
Output Filters
# Filter unmapped and low quality
bwa-mem2 mem -t 8 reference.fa r1.fq r2.fq | \
samtools view -@ 4 -bS -q 20 -F 4 - | \
samtools sort -@ 4 -o aligned.filtered.bam -Split Read Alignment
# For SV detection, use -Y for soft clipping
bwa-mem2 mem -t 8 -Y reference.fa r1.fq r2.fq > aligned.samMemory Requirements
- Index loading: ~10GB for human genome
- Per thread: ~1-2GB
- Typical human WGS: 30-50GB RAM with 8 threads
BWA-MEM (Alternative)
# Build index
bwa index reference.fa
# Paired-end alignment
bwa mem -t 8 reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam
# With read groups
bwa mem -t 8 -R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA' \
reference.fa reads_1.fq.gz reads_2.fq.gz > aligned.sam
# Direct to sorted BAM
bwa mem -t 8 -R '@RG\tID:sample1\tSM:sample1\tPL:ILLUMINA' \
reference.fa reads_1.fq.gz reads_2.fq.gz | \
samtools sort -@ 4 -o aligned.sorted.bam -BWA-MEM vs BWA-MEM2
| Feature | BWA-MEM | BWA-MEM2 |
|---|---|---|
| Status | Active | Archived |
| Speed | 1x | 2-3x faster |
| Index format | .bwt | .bwt.2bit.64 |
| Results | Baseline | Nearly identical |
| Memory | ~5GB | ~10GB |
Related Skills
- read-qc/fastp-workflow - Preprocess reads before alignment
- alignment-files/alignment-sorting - Post-alignment processing
- alignment-files/duplicate-handling - Mark duplicates
- variant-calling/variant-calling - Call variants from BAM
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