NGSTools

A compilation of tools for filtering and manipulating various NGS format written in the Scala language.

Author: Kyle Hernandez

Email: kmhernan@utexas.edu

========

Install

1. Download and install SBT (here)[http://www.scala-sbt.org/]
2. git clone https://github.com/kmhernan/scalaNGS.git or click the Download as zip file button to the right
3. Change to the scalaNGS folder
4. sbt update
5. sbt assembly
6. The jar executable will be in /target/scala-2.10/NGStool.jar
7. The accessory R script for plotting QC data is located /scripts/PlotQualityStats.R
   • This requires the following libraries: ggplot2, grid, and reshape2
   • Run from command-line as: Rscript PlotQualityStats.R <input.stat> </ouput/prefix/of/image>

General Usage:

java -jar NGSTools.jar -T/-TOOL <tool> [-h/--help]

Available tools:

• FilterReads - Filters NGS reads based on user-inputs.
• ReadStatistics - Creates a tab-delimited file containing various statistics, which can be fed into the accessory R-script PlotQualityStats.R

FilterReads Usage:

Solid reads

usage: java -jar NGSTools.jar -T FilterReads -P/-PLATFORM solid
                              -I/-INPUT file.csfasta file.qual -O/-OUTPUT file.csfasta file.qual
                              [-START Int] [-END Int] [-HPOLY Double] [-MINQ Int] [--MISSING] [-h/--help]

Required Arguments:
  -I/-INPUT	Input raw read files: <file.csfasta> <file.qual>
  -O/-OUTPUT	Output filtered read files: <file.csfasta> <file.qual>

Optional Arguments:
  -START	5' cut position (1-based index)
  -END		3' cut position (1-based index)
  -HPOLY	Relative length of repetitive base to consider a homopolymer.
  -MINQ	Minimum average quality score allowed.
  --MISSING	Removes reads with missing data, required for mapping reads.
  -h/--help	Print this message and exit.

Single-end Illumina

usage: java -jar NGSTools.jar -T FilterReads -P/-PLATFORM SE_illumina 
                              -I/-INPUT file.fastq -O/-OUTPUT file.fastq -QV-OFFSET {33,64}
                              [-START Int] [-END Int] [-HPOLY Double] [-MINQ Int] [-NMISSING Int]
                              [-POLYA Double Int] [-h/--help]
                              
Required Arguments:
  -I/-INPUT <String>	Input raw read files: <file.fastq> or <file.fastq.gz>
  -O/-OUTPUT <String>	Output filtered read files: <file.fastq>
  -QV-OFFSET <String>	Phred-scaled offset [33, 64]

Optional Arguments:
  -START <Int>		5' cut position (1-based index)
  -END <Int>		3' cut position (1-based index). Ex. AlfI: -START 1 -END 36
  -HPOLY <Double>	Relative length of repetitive base to consider a homopolymer. (Proportion of read length; e.g., between 0 and 1)
  -MINQ <Int>		Minimum average quality score allowed.
  -NMISSING <Int>	Lower limit for N's allowed.
  -POLYA <Double> <Int>	Takes two values:
        		  1) ProportionLimit [Double] - If a read has trailing A's of length <value> * sequence length, trim them.
        		  2) MinimumSize [Int] - If the trimmed sequence is shorter than <value>, remove it.
  -h/--help		Print this message and exit.

Paired-end Illumina

usage: java -jar NGSTools.jar -T FilterReads -P/-PLATFORM PE_illumina 
                              {-R1/-READ1 file_R1.fastq -R2/-READ2 file_R2.fastq | -INTER file_R1_R2.fastq} 
                              {-O1/-OUTREAD1 file_R1.fastq -O2/-OUTREAD2 file_R2.fastq | -OUT-INTER file_R1_R2.fastq}
                              -QV-OFFSET {33, 64} [-START Int] [-END Int] [-HPOLY Double] [-MINQ Int] [-NMISSING Int]
                              [-POLYA Double Int] [-h/--help]

Required Arguments:
Supports both separated and interleaved paired-end Fastq files.
If input Fastq files are separated (mate-pairs must be sorted in same order):
  -R1/-READ1 <String>	Input raw fastq file for first paired-end: <file_R1.fastq> or <file_R1.fastq.gz>
  -R2/-READ2 <String>	Input raw fastq file for second paired-end: <file_R2.fastq> or <file_R2.fastq.gz>

If input Fastq file is interleaved (pair 1 must always be followed by its mate-pair 2):
  -INTER <String>	Input raw fastq file containing both pairs: <file_R1_R2.fastq> or <file_R1_R2.fastq.gz>

Regardless of input format, reads can be written to either separated or interleaved fastq files:
  -O1/-OUTPUT1 <String>	Output separated fastq file for first paired-end: <file_R1.fastq>
  -O2/-OUTPUT2 <String>	Output separated fastq file for second paired-end: <file_R2.fastq>
  -OUT-INTER <String>	Output interleaved fastq file: <file_R1_R2.fastq>

  -QV-OFFSET <Int>	Phred-scaled offset [33, 64]

Optional Arguments:
  -START <Int>		5' cut position (1-based index)
  -END <Int>		3' cut position (1-based index). Ex. AlfI: -START 1 -END 36
  -HPOLY <Double>	Relative length of repetitive base to consider a homopolymer. (Proportion of read length; e.g., between 0 and 1)
  -MINQ <Int>		Minimum average quality score allowed.
  -NMISSING <Int>	Lower limit for N's allowed.
  -POLYA <Double> <Int>	Takes two values:
        		  1) ProportionLimit <Double> - If a read has trailing A's of length <value> * sequence length, trim them.
        		  2) MinimumSize <Int> - If the trimmed sequence is shorter than <value>, remove it.
  -h/--help		Print this message and exit.

ReadStatistics Usage:

usage: java -jar NGSTools.jar -T ReadStatistics -I/-INPUT file.fastq -QV-OFFSET [33,64] [-O/-OUTPUT file.txt] [-h/--help]

Required arguments:
  -I/-INPUT <String>	Input fastq file: <file.fastq> or <file.fastq.gz>
  -QV-OFFSET <Int>	Phred-scaled offset [33, 64]

Optional Arguments:
  -O/-OUTPUT <String>	Output stats file: <file.txt> [default stdout]
  -h/--help		Print this message and exit.