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Is Bio Read Alignment Bwa Alignment free to use?

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Who published Bio Read Alignment Bwa Alignment?

majiayu000 (@majiayu000) published this skill. Their other Agent Skills are listed on their SkillMD profile.

Bio Read Alignment Bwa Alignment by majiayu000

Name: Bio Read Alignment Bwa Alignment
Rating: 4.5 (4 reviews)
Author: majiayu000

File contents

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.pac

Basic 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.sam

Alignment 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.sam

Direct 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.bam

Mark 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.bam

Common 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.fq

Key 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.sam

Memory 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

---name: bio-read-alignment-bwa-alignmentdescription: Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.--- # BWA-MEM2 Alignment ## Build Index ```bash # 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.pac ``` ## Basic Alignment ```bash # 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.sam ``` ## Alignment with Read Groups ```bash # 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.sam ``` ## Direct to Sorted BAM ```bash # 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.bam ``` ## Mark Duplicates Pipeline ```bash # 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.bam ``` ## Common Options ```bash 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.fq ``` ## Key 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 ```bash # 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 ```bash # For SV detection, use -Y for soft clipping bwa-mem2 mem -t 8 -Y reference.fa r1.fq r2.fq > aligned.sam ``` ## Memory Requirements - Index loading: ~10GB for human genome - Per thread: ~1-2GB - Typical human WGS: 30-50GB RAM with 8 threads ## BWA-MEM (Alternative) ```bash # 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

Frequently asked questions