[med-svn] [ngila] 01/01: Wrong project ...
Andreas Tille
tille at debian.org
Wed Dec 13 20:13:16 UTC 2017
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tille pushed a commit to branch master
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commit 0845951af775924ed4112122aae881a5fbb4e551
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 13 21:12:36 2017 +0100
Wrong project ...
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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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