SmrtSeqTool

Sort,align,variant calling

SmrtSeqTool is a pipeline that sorts next-gen sequencing fastq files obtained from PACBIO platform by barcodes and aligns the barcode-sorted sequences to a reference sequence. The pipeline also identifies variants after sequence alignment.

• Sequence alignment and variant calling using Bowtie 2 and SAMtools/Bcftools.

Version

1.0.0

Tech

SmrtSeqTool uses a number of open source projects to work properly:

• Bowtie 2 - fast and sensitive read alignment
• Bcftools - utilities for variant calling and manipulating VCFs and BCFs
• SAMtools - for storing large nucleotide sequence alignments

Installation

The scripts are available at https://github.com/jinksrobertson/SJR_SMRTseq.git . To run the scripts, install Bowtie 2 and SAMtools/Bcftools are required to be installed. See corresponding websites listed above for installation instrucitons.

Using

The following files have to be supplied by the user and stored in the same directory as the SmrtSeqTool pipeline. ForBar.txt (forward barcodes, see format in sample_files) RevBar.txt (reverse barcodes, see format in sample_files) ref.txt (reference sequence, see format in sample_files) ccs.fastq (fastq files from PACBIO, NOTE: make sure to rename the file to "ccs.fastq")

To run the script:

$ bash sjrcan1.sh

Output file: "variants.txt" summarizing variants for each barcoded-sorted file.

To view individual alignement using SAMtool tview:

$ bash tview.sh

License

The MIT License(MIT)

Open source software