fq2SortedBAM: OpenOmics’ Genomics Secondary Analysis Pipeline

Overview:

The pipeline takes input fastq files and produces sorted BAM file through the following stages:

  1. Sequence Alignment: bwa-mem2 for short reads, mm2-fast (Accelerated Minimap2) for long reads (PacBio, ONT)
  2. SAMSort (Using SAMTools)

Modes:

fq2SortedBAM supports 4 different modes:

  1. sortedbam: It takes fastq reads files and reference genome as input and outputs sorted BAM file
  2. flatmode: It takes fastq reads files and reference genome as input, and outputs multiple (equal to the number of ranks created) unsorted SAM files
  3. fqprocessonly: Custom mode, not for general use
  4. multifq: Custom mode, not for general use

Use Docker

Docker build:

wget https://github.com/IntelLabs/Open-Omics-Acceleration-Framework/releases/download/3.0/Source_code_with_submodules.tar.gz  
tar -xzf Source_code_with_submodules.tar.gz  
cp Open-Omics-Acceleration-Framework/pipelines/fq2sortedbam/Dockerfile .
cp Open-Omics-Acceleration-Framework/pipelines/fq2sortedbam/config.yaml <inputdir>

docker save fq2bam:latest > fq2bam.tar     ## this step is optional  
docker build --build-arg http_proxy=$http_proxy --build-arg https_proxy=$https_proxy -t fq2bam .

Docker run:

docker load -i fq2bam.tar      ## optional, if the image is build on the same machine or is already loaded    
docker run  -v <readsdir>:/readsdir -v <outdir>:/outdir -v <refdir>:/refdir fq2bam:latest python run_fq2sortedbam.py --ref /refdir/<reference> --reads  /readsdir/<read1>  /readsdir/<read2>  --output /outdir/<outBAMfile>

Note:
<readsdir>: Location of the local directory containing read files read1 & read2
<refdir>: Location of the local directory containing reference sequence file ref
<outdir>: Location of the local directory for output files SAM/BAM

Use Source Code

Installation:

wget https://github.com/IntelLabs/Open-Omics-Acceleration-Framework/releases/download/3.0/Source_code_with_submodules.tar.gz  
tar -xzf Source_code_with_submodules.tar.gz  
cd Open-Omics-Acceleration-Framework/pipelines/fq2sortedbam/
bash install.sh <onprem/cloud>  ## onprem mode: Manually install the depenendies present in basic_setup_ubuntu.sh as it needs sudo access

Run:

python run_fq2sortedbam.py --ref <reference> --reads <read1> <read2> --output <outBAMfile>

General Notes:

  1. Individual pipeline tools are present in applications folder
  2. To understand various parameters to these tools, you can access their man page
  3. You can setup the parameters of these tools using params commandline option
  4. Understand all the parameters to fq3sortedbam using “-h” option
  5. fq2sortedbam supports the following aligners: a. DNA short read alignment using bwa-mem2
    b. DNA long read alignment using mm2-fast (minimap2)
    c. RNA short read alignment using STAR aligner
    d. bwa-meth based alignment