[med-svn] [ngsqctoolkit] 01/01: Provide some docs that can be downloaded from upstream - in case this package will ever be uploaded parts of this might be helpful

[Andreas Tille]

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commit 2a7304e14f00c4c5ba94bf81768d7ebfe61a0a5c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Dec 13 21:13:20 2017 +0100

    Provide some docs that can be downloaded from upstream - in case this package will ever be uploaded parts of this might be helpful
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+NGS QC Toolkit Manual
+TABLE OF CONTENTS
+1. Essential requirements .................................................................................... 2
+2. How to install additional perl modules ............................................................ 2
+3. How to use NGS QC Toolkit.............................................................................. 4
+4. Sample data ..................................................................................................... 4
+5. Tools in toolkit ................................................................................................. 5
+6. Detailed help information ................................................................................ 6
+(A) QC Tools ........................................................................................................ 6
+(B) Format-converter Tools ............................................................................... 11
+(C) Trimming Tools ............................................................................................ 13
+(D) Statistics Tools ............................................................................................ 15
+7. Sample commands......................................................................................... 16
+8. Contact details ............................................................................................... 18
+9. Citation .......................................................................................................... 18
+10.
+
+Acknowledgements .................................................................................... 18
+
+11.
+
+Terms of Use............................................................................................... 18
+
+1
+
+
1. Essential requirements
+
+
+
+
+
+Operating system:
+o Windows (PC)
+o Linux
+Software:
+o Perl (ActivePerl for Windows)
+Additional Perl modules required:
+o GD::Graph (optional, used to prepare graphs)
+o String::Approx (required to speed up the string matching for primer/adapter)
+
+2. How to install additional perl modules
+On Windows XP/Vista/7:
+Note: Activeperl (http://www.activestate.com/activeperl/downloads) has to be installed on
+windows.
+ Install perl modules using DOS command prompt. Following are the steps for installing
+GD::Graph
+(1) Open DOS command prompt and type “ppm-shell” and press enter. The “ppm>”
+prompt will come.
+
+(2) On “ppm” command prompt, the modules have to be searched using “search
+<module name>”. This will show all available modules for the given keyword with
+index number on left (In this case a single module is available for GD::Graph).
+
+2
+
+
(3) Install the module using “install <index number>” command.
+
+(4) And the module is installed.
+
+
+Following is the screenshot of String::Approx installation
+
+3
+
+
On Linux:
+Note: Check that perl has been installed on your system.
+Download modules from http://search.cpan.org
+Following are the web links for required modules:
+(1) GD::Graph
+(http://search.cpan.org/~bwarfield/GDGraph-1.44/Graph.pm)
+This module requires two dependencies:
+ GD
+(http://search.cpan.org/~lds/GD-2.45/GD.pm)
+ GD::Text
+(http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm)
+(2) String::Approx
+(http://search.cpan.org/~jhi/String-Approx-3.26/Approx.pm)
+Install these modules according to the “README” information provided with the module.
+
+3. How to use NGS QC Toolkit
+
+
+
+
+
+
+Download and install required software and perl modules
+Download source code from the home page (http://www.nipgr.res.in/ngsqctoolkit.html)
+Extract the compressed file
+Tools are available in the extracted folder
+Run these perl script using command “perl <tool name>”
+
+4. Sample data
+Sample input and output data is provided to download from the homepage of the NGS QC
+toolkit. Sample input data includes Illumina paired-end (~0.13 million reads), Illumina singleend (~0.13 million reads), 454 paired-end (~0.12 million reads) and 454 single-end (more than
+90 thousand reads) sequencing data. Sample output presents output of QC, trimming and
+statistics tools for above mentioned Illumina and 454 sample data. QC output contains highquality filtered data, text file and graphs for QC statistics and consolidated HTML report file.
+
+4
+
+
5. Tools in toolkit
+ QC
+o IlluQC.pl: Tool for quality control of sequencing data generated using Illumina
+platform (FASTQ format)
+o IlluQC_PRLL.pl: This tool has the same functionality as IlluQC.pl. However, it
+provides an additional option to use multiple CPUs to speed up the analysis
+o 454QC.pl: Tool for quality control of sequencing data generated using 454
+platform (read and quality in FASTA format)
+o 454QC_PRLL.pl: Tool performs same quality control analysis as 454QC.pl and
+helps to analyze data using multiple CPUs
+o 454QC_PE.pl: Tool for quality control of paired-end sequencing data generated
+using 454 platform (read and quality in FASTA format)
+
+ Format-converter
+o SangerFastqToIlluFastq.pl: To convert fastq-sanger variant to fastq-illumina
+variant of FASTQ format
+o SolexaFastqToIlluFastq.pl: To convert fastq-solexa variant to fastq-illumina
+variant of FASTQ format
+o FastqTo454.pl: To convert FASTQ format (any variant) to 454 format (two files in
+FASTA format: one for reads/sequences (.fna) and another for quality (.qual))
+o FastqToFasta.pl: To convert FASTQ format file to FASTA format file for
+reads/sequences
+
+ Trimming
+o TrimmingReads.pl: Tool for trimming reads from 5’ and/or 3’ end of the read
+(FASTQ or FASTA format)
+o HomoPolymerTrimming.pl: Tool for trimming 3’ end of the reads from the first
+base of homopolymer of given length
+o AmbiguityFiltering.pl: Tool for filtering reads containing ambiguous bases or
+trimming flanking ambiguous bases
+
+ Statistics
+o AvgQuality.pl: Tool to calculate average quality score for each read and overall
+quality score for the given FASTA quality file
+o N50Stat.pl: Tool to generate statistics for read/sequence data given in FASTA
+format
+
+5
+
+
6. Detailed help information
+Following is the detailed help for each tool provided in the NGS QC Toolkit.
+
+(A) QC Tools
+(1) IlluQC.pl: This tool performs quality check and filtering of the sequencing data
+generated using Illumina technology. Input to this tool is FASTQ files (any variant)
+containing read and corresponding quality scores. Following are the options
+available with IlluQC.pl.
+Usage: perl IlluQC.pl <options>
+IlluQC.pl options:
+### Input reads (FASTQ) options (Atleast one option is required)
+-pe <Forward reads file> <Reverse reads file> <Primer/Adaptor
+library> <FASTQ variant>
+Paired-end read files (FASTQ) with primer/adaptor library and
+FASTQ variant
+User may choose from the provided primer/adaptor library or can
+give a file containing primer/adaptor sequences, one per line
+Multiple libraries can be given using multiple '-pe' options
+For eg.: -pe r1.fq r2.fq 3 1 -pe t1.fq t2.fq 2 A
+-se <Reads file> <Primer/Adaptor library> <FASTQ variant>
+Single-end read file (FASTQ) with primer/adaptor library and
+FASTQ variant
+Multiple libraries can be given using multiple '-se' options
+For eg.: -se r1.fq 3 2 -se t2.fq 2 2
+Primer/Adaptor libraries:
+1 = Genomic DNA/Chip-seq Library
+2 = Paired End DNA Library
+3 = DpnII gene expression Library
+4 = NlaIII gene expression Library
+5 = Small RNA Library
+6 = Multiplexing DNA Library
+N = Do not filter for Primer/Adaptor
+<File> = File for user defined primer/adaptor sequences, one
+per line
+FASTQ
+1 =
+2 =
+3 =
+4 =
+5 =
+A =
+
+variants:
+Sanger (Phred+33, 33 to 73)
+Solexa (Phred+64, 59 to 104)
+Illumina (1.3+) (Phred+64, 64 to 104)
+Illumina (1.5+) (Phred+64, 66 to 104)
+Illumina (1.8+) (Phred+33, 33 to 74)
+Automatic detection of FASTQ variant
+
+### Other options [Optional]
+-h | -help
+Prints this help
+---------------------------- QC Options ----------------------------
+
+6
+
+
-l | -cutOffReadLen4HQ <Real number, 0 to 100>
+The cut-off value for percentage of read length that should be
+of given quality
+default: 70
+-s | -cutOffQualScore <Integer, 0 to 40>
+The cut-off value for PHRED quality score for high-quality
+filtering
+default: 20
+------------------------ Processing Options ------------------------p | -processes <Integer>
+Number of processes to be used
+default: 1
+-onlyStat
+Outputs only statistics without filtered data output
+-------------------------- Output Options --------------------------t | -statOutFmt <Integer>
+Output format for statistics
+Formats:
+1 = formatted text
+2 = tab delimited
+default: 1
+-o | -outputFolder <Output folder name/path>
+Output will be stored in the given folder
+default: By default, output folder (IlluQC_Filtered_files) will
+be generated where the input files are
+-z | -outputDataCompression <Character>
+Output format for HQ filtered data
+Formats:
+t = text FASTQ files
+g = gzip compressed files
+default: t
+
+Output: IlluQC.pl generates statistics for quality check and filtering steps along with
+quality of input and high-quality filtered data in the form of text files and graphs.
+Following are the sample output graphs showing the average quality score at each
+base position (A), GC content distribution (B), average quality distribution (C) and
+base composition (D) for input and filtered reads. (E) shows the percentage of reads
+for different quality score ranges at each base position. The pie chart shows the summary
+of quality control analysis (F).
+
+7
+
+
A
+
+C
+
+B
+
+E
+
+D
+
+F
+
+(2) 454QC.pl: This tool requires two files as an input: 1) .fna file containing
+reads/sequences in FASTA format and 2) .qual file containing quality score in FASTA
+format. On the basis of quality provided in the second file the quality check is
+performed and reads are filtered. Following is the detailed help for 454QC.pl.
+Usage: perl 454QC.pl <options>
+454QC.pl options:
+### Input reads (FASTA format; .fna and .qual files) (Required)
+-i <Read file> <Quality file> <Primer/Adaptor library>
+Read and quality file in FASTA format with primer/adaptor
+library
+User may choose from the provided primer/adaptor library or can
+give a file containing primer/adaptor sequences, one per line
+Multiple libraries can be given using multiple '-i' options
+For eg.: -i read1.fna read1.qual 3 -i read2.fna read2.qual 2
+Primer/Adaptor libraries:
+1 = Rapid Library (Standard)
+
+8
+
+
2 = Paired End Library
+3 = Amplicon PE Library
+4 = Small RNA Library
+N = Do not filter for Primer/Adaptor
+<File> = File for user defined primer/adaptor sequences, one
+per line
+### Other options [Optional]
+-h | -help
+Prints this help
+---------------------------- QC Options ----------------------------l | -cutOffReadLen4HQ <Real number, 0 to 100>
+The cut-off value for percentage of read length that should be
+of given quality
+default: 70
+-s | -cutOffQualScore <Integer, 0 to 40>
+The cut-off value for PHRED quality score for high-quality
+filtering
+default: 20
+-n | -homoPolyLen <Integer>
+Minimum length of the homopolymer to be trimmed (0: to skip the
+homopolymer trimming)
+For eg.: -n 8, will trim the right end of read from the
+homopolymer of at least 8 bases long
+default: 0 (homopolymer trimming is off)
+-m | -minLen <Integer>
+Filter sequences shorter than the given minimum length
+default: 100
+-f | -lenFilter <Y/N>
+Are sequences to be filtered on the basis of length: (Y)es or
+(N)o
+default: Y
+------------------------ Processing Options ------------------------p | -processes <Integer>
+Number of processes to be used
+default: 1
+-onlyStat
+Outputs only statistics without filtered data output
+-------------------------- Output Options --------------------------t | -statOutFmt <Integer>
+Output format for statistics
+Formats:
+1 = formatted text
+2 = tab delimited
+default: 1
+-o | -outputFolder <Output folder name/path>
+Output will be stored in the given folder
+default: By default, output folder (454QC_Filtered_files) will
+be generated where the input files are
+-z | -outputDataCompression <Character>
+Output format for HQ filtered data
+Formats:
+t = text FASTA files
+g = gzip compressed files
+default: t
+
+9
+
+
Output: 454QC.pl generates statistics after each step of analysis (number and
+percentage of trimmed, trashed and high-quality reads) and statistics for both input
+and filtered data (minimum, maximum, mean, N25, N50, N75, N90 and N95 read
+length) in the form of text files and graphs including average quality distribution (A),
+GC content distribution (B) and average length distribution (C) and base composition
+(D) for input and filtered data. The pie charts summarize the quality control analysis
+(E).
+
+A
+
+B
+
+C
+
+D
+
+E
+
+(3) IlluQC_PRLL.pl: This tool provides a utility to process input data parallely on multiple
+CPUs (using ‘-c’ option) to speed-up the quality control analysis. Otherwise, it is
+identical to the IlluQC.pl in context of algorithm for processing Illumina data.
+
+10
+
+
(4) 454QC_PRLL.pl: This tool can use multiple CPUs (using ‘-c’ option) and process the
+large amount of data very fast. It performs same function as 454QC.pl for quality
+control of 454 sequencing data.
+(5) 454QC_PE.pl: This tool performs quality control of paired-end sequencing data
+generated using 454 platform. It identifies the linker sequence to separate the PE
+reads as first step. The following steps of QC on these PE reads and unpaired reads
+(where linker sequence could not be identified) are same as other 454QC tools.
+
+(B) Format-converter Tools
+(1) SangerFastqToIlluFastq.pl: A tool for the conversion of FASTQ file containing quality
+score encoded in fastq-sanger format (score: 33 to 73) to the FASTQ file having
+quality score encoded in fastq-illumina format (score: 64 to 104). Following are the
+options provided with this tool.
+Usage: perl SangerFastqToIlluFastq.pl <options>
+SangerFastqToIlluFastq.pl options:
+### Input reads (FASTQ) (Required)
+-i <Sanger FASTQ read file>
+Read file in Sanger FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, file will be stored where the input file is
+
+(2) SolexaFastqToIlluFastq.pl: A tool for the conversion of FASTQ file containing quality
+score encoded in fastq-solexa format (score: 59 to 73) to the FASTQ file having
+quality score encoded in fastq-illumina format (score: 64 to 104). Following are the
+options provided with this tool.
+Usage: perl SolexaFastqToIlluFastq.pl <options>
+SolexaFastqToIlluFastq.pl options:
+### Input reads (FASTQ) (Required)
+-i <Solexa FASTQ read file>
+Read file in Solexa FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFile <Output file name>
+Output will be stored in the given file
+
+11
+
+
default: By default, file will be stored where the input file is
+
+(3) FastqTo454.pl: This tool converts FASTQ format file (any variant) to 454 format, i.e.
+separates reads/sequences and quality in different FASTA files (.fna and .qual).
+Options provided with the tool:
+Usage: perl FastqTo454.pl <options>
+FastqTo454.pl options:
+### Input reads (FASTQ) (Required)
+-i <Illumina FASTQ read file>
+Read file in Illumina FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFolder <Output folder name>
+Output will be stored in the given folder
+default: By default, files will be stored where the input file
+is
+-v | -fastqVariant <FASTQ variant>
+FASTQ variants:
+1 = Sanger (Phred+33, 33 to 73)
+2 = Solexa (Phred+64, 59 to 104)
+3 = Illumina (1.3+) (Phred+64, 64 to 104)
+4 = Illumina (1.5+) (Phred+64, 66 to 104)
+5 = Illumina (1.8+) (Phred+33, 33 to 74)
+A = Automatic detection of FASTQ variant
+default: "A"
+
+(4) FastqToFasta.pl: It exports reads/sequences from the FASTQ file to the FASTA
+format file. Following are the options available with the tool.
+Usage: perl FastqToFasta.pl <options>
+FastqToFasta.pl options:
+### Input reads (FASTQ) (Required)
+-i <FASTQ read file>
+Read file in FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, file will be stored where the input file is
+
+12
+
+
(C) Trimming Tools
+(1) TrimmingReads.pl: This tool trims the reads/sequences and their quality scores (in
+case of FASTQ file) in two ways. First, it trims fixed (user-specified) number of bases
+from 5’ and/or 3’ end of the reads and corresponding qualities from the input FASTQ
+file. Second, it trims low quality bases from 3’ end of the read using user-defined
+threshold value of quality score. Input to this tool is either FASTQ or FASTA format
+file. Options are provided to specify the number of bases to be trimmed and the
+quality threshold for quality based trimming.
+Usage: perl ..\TrimmingReads.pl <options>
+..\TrimmingReads.pl options:
+### Input reads/sequences (FASTQ/FASTA) (Required)
+-i <Forward read/sequence file>
+File containing reads/sequences in either FASTQ or FASTA format
+### Input reads/sequences (FASTQ) [Optional]
+-irev <Reverse read/sequence file of paired-end data>
+File containing reverse reads/sequences of paired-end data in
+FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+--------------------------------- Trimming Options --------------------------------l | -leftTrimBases <Integer>
+Number of bases to be trimmed from left end (5' end)
+default: 0
+-r | -rightTrimBases <Integer>
+Number of bases to be trimmed from right end (3' end)
+default: 0
+-q | -qualCutOff <Integer> (Only for FASTQ files)
+Cut-off PHRED quality score for trimming reads from right end
+(3' end)
+For eg.: -q 20, will trim bases having PHRED quality score
+less than 20 at 3' end of the read
+Note: Quality trimming can be performed only if -l and -r are
+not used
+default: 0 (i.e. quality trimming is OFF)
+-n | -lenCutOff <Integer>
+Read length cut-off
+Reads shorter than given length will be discarded
+default: -1 (i.e. length filtering is OFF)
+--------------------------------- Output Options --------------------------------o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, output file will be stored where the input
+file is
+
+13
+
+
(2) HomoPolymerTrimming.pl: The tool finds homopolymer of the given length and
+trims the 3’ end of reads/sequences from the first base of the homopolymer from
+the data in FASTA format.
+Usage: perl HomopolymerTrimming.pl <options>
+HomopolymerTrimming.pl options:
+### Input reads/sequences (FASTA format; .fna and .qual files)
+(Required)
+-i <Read/Sequence file> [Quality file (optional)]
+Read/Sequence and quality file in FASTA format
+### Other options [Optional]
+-h | -help
+Prints this help
+-l | -minReadLen <Integer>
+Minimum length of a read/sequence to be retained in output
+default: 100
+-n | -homoPolyLen <Integer>
+Minimum length of the homopolymer to be trimmed
+For eg.: -n 8, will trim the right end of read/sequence from
+the homopolymer of at least 8 bases long
+Note:- use -n 0 to skip homopolymer trimming (for only length
+filtering)
+default: 8
+-o | -outputFolder <Output folder name/path>
+Output will be stored in the given folder
+default: By default, files will be stored where the input files
+are
+
+(3) AmbiguityFiltering.pl: The tool helps filtering ambiguous base content in two ways:
+1) Trimming 5’ and/or 3’ ambiguous bases, and 2) Filtering reads based on user
+defined cut-off values for maximum number/percentage of allowed ambiguous
+bases.
+Usage: perl ..\AmbiguityFiltering.pl <options>
+..\AmbiguityFiltering.pl options:
+### Input reads/sequences (FASTQ/FASTA) (Required)
+-i <Forward read/sequence file>
+File containing reads/sequences in either FASTQ or FASTA format
+### Input reads/sequences (FASTQ) [Optional]
+-irev <Reverse read/sequence file of paired-end data>
+File containing reverse reads/sequences of paired-end data in
+FASTQ format
+### Other options [Optional]
+-h | -help
+Prints this help
+--------------------------------- Trimming Options --------------------------------c | -countN <Integer>
+
+14
+
+
Maximum number of allowed ambiguous bases
+default: 0
+-p | -percentN <Integer>
+Maximum percentage of allowed ambiguous bases
+default: 0
+-t5 | -trim5EndN
+Trim ambiguous bases from 5' end of the sequence
+default: off
+-t3 | -trim3EndN
+Trim ambiguous bases from 3' end of the sequence
+default: off
+-n | -lenCutOff <Integer>
+Sequence length cut-off
+Sequences shorter than given length will be discarded
+default: -1 (i.e. length filtering is OFF)
+NOTE: filtering can be performed using any one of (-c), (-p) and (t5 and/or -t3) switches at a time
+--------------------------------- Output Options --------------------------------o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, output file will be stored where the input
+file is
+
+(D) Statistics Tools
+(1) AvgQuality.pl: Tool calculates average quality score for each read and overall
+average quality score for the given file. This tool takes a quality file in FASTA format
+as an input.
+Usage: perl AvgQuality.pl <options>
+AvgQuality.pl options:
+### Input quality (FASTA) (Required)
+-i <Quality file>
+Quality file in FASTA format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, quality statistics file will be stored
+where the input file is
+
+(2) N50Stat.pl: This tool calculates different statistics for read file given in FASTA
+format. It calculates total number of reads/sequences, total and individual (A,T,C,G
+and N) number of bases, G+C and A+T counts, and minimum, maximum, average,
+median, N25, N50, N75, N90 and N95 read/sequence length. Following are the
+options provided for this tool.
+Usage: perl N50Stat.pl <options>
+
+15
+
+
N50Stat.pl options:
+### Input reads/sequences (FASTA) (Required)
+-i <Read/Sequence file>
+Read/Sequence in fasta format
+### Other options [Optional]
+-h | -help
+Prints this help
+-o | -outputFile <Output file name>
+Output will be stored in the given file
+default: By default, N50 statistics file will be stored where
+the input file is
+
+7. Sample commands
+
+
+For quality control analysis of two paired-end sequencing data (pe11.fq-pe12.fq and
+pe21.fq-pe22.fq) and two single-end sequencing data (se1.fq and se2.fq) from Illumina
+platform using default parameters except statistics in tab-delimited file format:
+perl IlluQC.pl -pe pe11.fq pe12.fq 2 A -pe pe21.fq pe22.fq
+2 A -se se1.fq 1 1 -se se2.fq 1 A -statOutFmt 2 -p 4
+Options used:
+-pe pe11.fq pe12.fq 2 A: The first paired read data is inputted using -pe switch followed
+by file names for both the ends followed by the primer/adaptor library used in
+sequencing (2 = Paired-End DNA Library) and FASTQ variant (A = Automatic detection
+of FASTQ variant)
+-se se1.fq 1 1: For single-end sequencing data, -se switch is used followed by name of
+the read file followed by the primer/adaptor library used (1 = Genomic DNA/Chip-seq
+Library) and FASTQ variant (1 = Sanger (Phred+33, 33 to 73))
+
+-p 4: This option state the number of processes to be used. All four read data are
+processed simultaneously. For instance, the value “2” for this switch will process two
+datasets concurrently.
+-statOutFmr 2: The statistics will be printed in a tab-delimited file format.
+
+16
+
+
This command will perform quality control and filtering of two paired-end and two
+single-end sequencing datasets simultaneously (-p 4, four libraries are processed all
+together). The filtered files are generated where the input files are.
+
+
+For quality control analysis without primer/adaptor contamination removal for two 454
+datasets (lib1.fna-lib1.qual and lib2.fna-lib2.qual):
+perl 454QC.pl -i lib1.fna lib1.qual n -i lib2.fna lib2.qual
+n -n 7 -o FilteredFiles
+Options used:
+-i lib1.fna lib1.qual n: The switch -i is used to input read and quality files (FASTA format)
+of 454 sequencing data followed by the primer/adaptor library used for sequencing (n,
+skips the primer/adaptor filtering step)
+-n 7: The switch -n states the minimum length of the homopolymer to be trimmed. This
+will trim reads from the first base of homopolymer (at least 7 base pairs in length).
+-o FilteredFiles: A folder will be created in the current directory and the resulting filtered
+and statistics files are stored in it.
+
+17
+
+
8. Contact details
+Ravi Patel (ravi_patel_4 at yahoo.co.in)
+Mukesh Jain (mjain at nipgr.res.in)
+
+9. Citation
+If toolkit has been used for any publication, please cite as below
+Patel RK, Jain M (2012). NGS QC Toolkit: A toolkit for quality control of next generation
+sequencing data. PLoS ONE, 7(2): e30619. (http://www.nipgr.res.in/ngsqctoolkit.html)
+
+10. Acknowledgements
+We gratefully acknowledge the team members at Genotypic Technology for help and
+discussion with their SeqQC (http://genotypic.co.in/SeqQC.html?mnu=1) tool. We are also
+thankful to the anonymous reviewers and users of NGS QC Toolkit for the useful
+suggestions for its improvement.
+
+11. Terms of Use
+NGS QC Toolkit has been developed at National Institute of Plant Genome Research,
+Aruna Asaf Ali Marg, New Delhi – 110067, India. All rights about the toolkit are reserved to
+National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi – 110067,
+India.
+NGS QC Toolkit is a free and open source software toolkit, and distributed in the hope
+that it will be useful. In no event will NIPGR be liable to you for damage, including any
+general, special, consequential or incidental damage arising out of the use, modification or
+inability to use the program (including but not limited to loss of data or data being rendered
+inaccurate or losses sustained by you or third parties or a failure of the program to operate
+with any other programs). NGS QC Toolkit can be used, redistributed and/or modified freely
+for non-commercial purposes subject to the original source is properly cited.
+THIS PACKAGE IS PROVIDED “AS IS” AND WITHOUT WARRANTY OF ANY KIND, EITHER
+EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+Use of this toolkit is taken as an agreement to these terms of usage.
+
+18
+
+

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