Generate BAM/CRAM output given one or more pairs of FASTQ files by using Parabricks

fq2bam (FQ2BAM + BWA-MEM)

Parabricks fq2bam is a software tool that can generate BAM/CRAM output from one or more pairs of FASTQ files. This tool takes advantage of the parallel computing capabilities of GPUs to speed up the analysis process.

To use Parabricks, users can provide input files in FASTQ format and specify the reference genome they wish to use for alignment. The software uses a proprietary algorithm to perform read alignment, variant calling, and quality control. The output is then generated in BAM or CRAM format, depending on the user's preference.

In this case study, we will align our sample and reference genome for further comparison and analysis. Following is our reference genome.

Reference Genome: human_g1k_v37.fasta

Sample Data Source: SRA SRR7733443

Number Of Read: 2 x 5M bp

Read length: 150bp

We followed the steps below to collect the performance results:

First, we need to use the scratch directory. Please prepare about 50GB of free space for this experiment.

We have prepared samples and their index in OAsis. You may skip steps 1 to 4 by utilizing them.
To utilize the prepared data, run: cp /pfss/toolkit/parabricks_data $SCRATCH/parabracks

Download the sample genome for analysis.
1. Download the SRA toolkit from https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software#header-global
2. tar xfzv sratoolkit.2.10.5-centos_linux64.tar.gz
3. sratoolkit.2.10.5-centos_linux64/bin/fastq-dump -X 5000000 --split-files SRR9932168
Download the reference genome.
1. Download reference from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz

Index the genome.

Leverage our Parabricks container, which already includes samtools.

singularity run --nv /pfss/containers/clara-parabricks.4.0.0-1.sif bash samtools faidx /human_g1k_v37.fasta

install bwa and use it to index human_g1k_v37.fasta

# install bwa
git clone https://github.com/lh3/bwa.git
cd bwa
make

# request a compute node to perform the indexing
srun --pty -p batch --cpus-per-task=32  --mem=100G bash

# in the prompt, run:
./bwa index ../human_g1k_v37.fasta

Download Known Site
1. download 00-common_all.vcf from https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b150_GRCh37p13/VCF/
2. singularity run /pfss/containers/gatk.sif gatk IndexFeatureFile -I /00-common_all.vcf

Run Parabricks

We utilize one NVIDIA A100 here, be careful that Parabricks currently does not support MIG.

srun --pty -p gpu --cpus-per-task=16 --gres=gpu:a100:1 --mem=128G bash
singularity run --nv /pfss/containers/clara-parabricks.4.1.0-1.sif bash

cd $SCRATCH/parabricks

mkdir tmp

NVIDIA_VISIBLE_DEVICES="0" pbrun fq2bam \
  --num-gpus 1 \
  --ref ./human_g1k_v37.fasta \
  --in-fq ./SRR9932168_1.fastq ./SRR9932168_2.fastq \
  --out-bam ./mark_dups_gpu.bam \
  --tmp-dir ./tmp \
  --knownSites ./00-common_all.vcf \
  --out-recal-file ./recal_gpu.txt

Result
1. The output should be something like this:
2. main] CMD: /usr/local/parabricks/binaries//bin/bwa mem -Z ./pbOpts.txt /pfss/scratch02/appcara/parabricks/parabricks_sample/Ref/human_g1k_v37.fasta /pfss/scratch02/appcara/parabricks/sratoolkit.3.0.6-centos_linux64/SRR9932168_1.fastq /pfss/scratch02/appcara/parabricks/sratoolkit.3.0.6-centos_linux64/SRR9932168_2.fastq @RG\tID:SRR9932168.1.1\tLB:lib1\tPL:bar\tSM:sample\tPU:SRR9932168.1.1
  [main] Real time: 105.672 sec; CPU: 1343.564 sec
  [PB Info 2023-Aug-01 12:07:41] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:41] || Program: GPU-BWA mem, Sorting Phase-I ||
  [PB Info 2023-Aug-01 12:07:41] || Version: 4.0.0-1 ||
  [PB Info 2023-Aug-01 12:07:41] || Start Time: Tue Aug 1 12:05:55 2023 ||
  [PB Info 2023-Aug-01 12:07:41] || End Time: Tue Aug 1 12:07:41 2023 ||
  [PB Info 2023-Aug-01 12:07:41] || Total Time: 1 minute 46 seconds ||
  [PB Info 2023-Aug-01 12:07:41] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:41] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:41] || Parabricks accelerated Genomics Pipeline ||
  [PB Info 2023-Aug-01 12:07:41] || Version 4.0.0-1 ||
  [PB Info 2023-Aug-01 12:07:41] || Sorting Phase-II ||
  [PB Info 2023-Aug-01 12:07:41] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:41] progressMeter - Percentage
  [PB Info 2023-Aug-01 12:07:41] 0.0 0.00 GB
  [PB Info 2023-Aug-01 12:07:51] Sorting and Marking: 10.001 seconds
  [PB Info 2023-Aug-01 12:07:51] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:51] || Program: Sorting Phase-II ||
  [PB Info 2023-Aug-01 12:07:51] || Version: 4.0.0-1 ||
  [PB Info 2023-Aug-01 12:07:51] || Start Time: Tue Aug 1 12:07:41 2023 ||
  [PB Info 2023-Aug-01 12:07:51] || End Time: Tue Aug 1 12:07:51 2023 ||
  [PB Info 2023-Aug-01 12:07:51] || Total Time: 10 seconds ||
  [PB Info 2023-Aug-01 12:07:51] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:51] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:51] || Parabricks accelerated Genomics Pipeline ||
  [PB Info 2023-Aug-01 12:07:51] || Version 4.0.0-1 ||
  [PB Info 2023-Aug-01 12:07:51] || Marking Duplicates, BQSR ||
  [PB Info 2023-Aug-01 12:07:51] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:07:51] progressMeter - Percentage
  [PB Info 2023-Aug-01 12:08:01] 0.0 4.38 GB
  [PB Info 2023-Aug-01 12:08:11] 0.0 4.38 GB
  [PB Info 2023-Aug-01 12:08:21] 0.0 4.38 GB
  [PB Info 2023-Aug-01 12:08:31] 0.0 4.38 GB
  [PB Info 2023-Aug-01 12:08:41] 0.0 4.38 GB
  [PB Info 2023-Aug-01 12:08:51] 3.4 4.28 GB
  [PB Info 2023-Aug-01 12:09:01] 100.0 0.00 GB
  [PB Info 2023-Aug-01 12:09:01] BQSR and writing final BAM: 70.031 seconds
  [PB Info 2023-Aug-01 12:09:01] ------------------------------------------------------------------------------
  [PB Info 2023-Aug-01 12:09:01] || Program: Marking Duplicates, BQSR ||
  [PB Info 2023-Aug-01 12:09:01] || Version: 4.0.0-1 ||
  [PB Info 2023-Aug-01 12:09:01] || Start Time: Tue Aug 1 12:07:51 2023 ||
  [PB Info 2023-Aug-01 12:09:01] || End Time: Tue Aug 1 12:09:01 2023 ||
  [PB Info 2023-Aug-01 12:09:01] || Total Time: 1 minute 10 seconds ||
  [PB Info 2023-Aug-01 12:09:01] ------------------------------------------------------------------------------

fq2bam performs the following steps.

Compatible CPU-based BWA-MEM, GATK4 Commands

srun --pty -p batch --cpus-per-task=32  --mem=100G bash
singularity run /pfss/containers/gatk.4.4.0.0.sif bash

cd $SCRATCH
cd bwa

./bwa mem -t 32 -K 10000000 -R '@RG\tID:SRR9932168.1.1 \tLB:lib1\tPL:bar\tSM:sample\tPU:SRR9932168.1.1 ' \
../human_g1k_v37.fasta \
../SRR9932168_1.fastq \
../SRR9932168_2.fastq | \
gatk SortSam \
--java-options -Xmx30g \
--MAX_RECORDS_IN_RAM 5000000 \
-I /dev/stdin \
-O ../cpu.bam \
--SORT_ORDER coordinate

# for max spot id 5000000 spent 2.72 mins for sorting, 2.2 mins for convert to BAM

[main] CMD: ./bwa mem -t 32 -K 10000000 -R @RG\tID:SRR9932168.1.1 \tLB:lib1\tPL:bar\tSM:sample\tPU:SRR9932168.1.1  /pfss/scratch02/appcara/parabricks/parabricks_sample/Ref/human_g1k_v37.fasta /pfss/scratch02/appcara/parabricks/sratoolkit.3.0.6-centos_linux64/SRR9932168_1.fastq /pfss/scratch02/appcara/parabricks/sratoolkit.3.0.6-centos_linux64/SRR9932168_2.fastq
[main] Real time: 151.130 sec; CPU: 3594.553 sec
INFO    2023-08-01 05:58:33     SortSam Finished reading inputs, merging and writing to output now.
INFO    2023-08-01 05:58:47     SortSam Wrote    10,000,000 records from a sorting collection.  Elapsed time: 00:02:43s.  Time for last 10,000,000:   14s.  Last read position: */*
[Tue Aug 01 05:58:47 GMT 2023] picard.sam.SortSam done. Elapsed time: 2.72 minutes.
Runtime.totalMemory()=1409286144
Tool returned:
0
# generate .dict file 
cd $SCRATCH
gatk CreateSequenceDictionary -R human_g1k_v37.fasta

# Mark duplicates.

gatk MarkDuplicates \
--java-options -Xmx30g \
-I ./cpu.bam \
-O ./mark_dups_cpu.bam \
-M metrics.txt

# spend 1 mins

# Generate a BQSR report.

gatk IndexFeatureFile -I ./00-common_all.vcf

gatk BaseRecalibrator \
--java-options -Xmx30g \
--input ./mark_dups_cpu.bam \
--output ./recal_cpu.txt \
--known-sites ./00-common_all.vcf \
--reference ./human_g1k_v37.fasta

# spend 1.68 mins

One of the main advantages of Parabricks is its speed. The software can analyze large datasets in a fraction of the time it would take traditional tools to complete the same task. Parabricks is also highly scalable and can analyze datasets of varying sizes without sacrificing performance. It is ideal for researchers and scientists who need to process large amounts of genomic data quickly and efficiently.

View bam file in IGV

First, start a VNC container, and load module IGV in terminal, after that you can use igv.sh to run IGV

You can use igvtools to index the bam file