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STRoNGS

A tool for profiling of STRs using next-generation sequencing data

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• STRoNGS
  • Installation
    • Requirements
    • Download and install in Unix
  • Usage for Windows
    • Right click on the image and select "Open Image in New Tab"
  • Usage for Linux
    • Required arguments
    • Optional arguments
    • Input
    • Output
  • Example workflows
    • STRoNGS running

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Installation

Requirements

≥ Java 1.7

 

Download and install in Unix

> wget -r https://sourceforge.net/projects/strongs2016/files/latest/download?source=files
> tar -zxvf 

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Usage for Windows

Right click on the image and select "Open Image in New Tab"

Usage for Linux

usage: java -jar STRoNGS-X.X.jar [options]

 

Required arguments

    -1, --read1   FILE  RNA sequencing read1 file
    -r, --ref     PATH  reference file path
    -m, --marker  FILE  marker information file

 

Optional arguments

    -2, --read2         FILE  RNA sequencing read2 file
    -o, --outDir        DIR   output directory
    -l, --prim          INT   primer length default=15

 

Input

• STRoNGS requires raw FASTQ file or compressed form of FASTQ.GZ as input format. It can be use a single or paired files.

 

Output

STRoNGS produces *.typing.txt tab-delimited TXT file.

• Locus : STR locus id
• P_Allele : Detected STR allele by pattern typing
• S_Allele : Detected STR allele by length typing
• Flank5 : upstream flanking region sequence with variant
• RepeatPattern : Detected repeat structure with variant
• Flank3 : downstream flanking region sequence with variant
• Ratio : Fraction of supported read for the allele in the locus
• #Reads : Count of supported read for the allele in the locus
• TotalReads : Total read count in the locus
• Representational Read ID : Rpresentative read id

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Example workflows

STRoNGS running

java -jar STRoNGS-X.X.jar \
    -1 sample_1.fastq \
    -2 sample_2.fastq \
    -r /path/reference \
    -m /path/marker.txt

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Project Members:

• Sora Kim (admin)