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This command line tool can be downloaded as part of the library: http://genome.sph.umich.edu/wiki/Software#Download
This command line tool can be downloaded as part of the library: http://genome.sph.umich.edu/wiki/Software#Download
Note: Since the FastQValidator checks for unique sequence names, it may use a large amount of memory.
Note: Since the FastQValidator checks for unique sequence names, it may use a large amount of memory - this can be disabled by specifying the --disableSeqIDCheck option
== Valid FastQ File Requirements ==
== Valid FastQ File Requirements ==
overwrites the printableErrors option.
overwrites the printableErrors option.
--baseComposition : Print the Base Composition Statistics.
--baseComposition : Print the Base Composition Statistics.
--disableSeqIDCheck : Disable the unique sequence identifier check.
Use this option to save memory since the sequence id
check uses a lot of memory.
Does not affect the printing of Base Composition Statistics.
--quiet : Suppresses the display of errors and summary statistics.
--quiet : Suppresses the display of errors and summary statistics.
Does not affect the printing of Base Composition Statistics.
Does not affect the printing of Base Composition Statistics.
=== Usage ===
=== Usage ===
./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxErrors <numErrors>] [--printableErrors <printableErrors>|--ignoreErrors] [--baseComposition] [--disableSeqIDCheck] [--quiet] [--baseSpace|--colorSpace|--auto] [--params]
=== Examples ===
=== Examples ===
== FastQ Validator Output ==
== FastQ Validator Output ==
When running the fastQValidator Executable, the output starts with a summary of the parameters:
When running the fastQValidator Executable, if the --params option is specified, the output starts with a summary of the parameters:
The following parameters are in effect:
The following parameters are available. Ones with "[]" are in effect:
Input Parameters
Input Parameters
--file [../fastqValidator/test/testFile.txt], --baseComposition,
--disableSeqIDCheck, --quiet, --params [ON], --minReadLen [10],
--maxErrors [-1]
--maxErrors [-1]
Space Type : --baseSpace [ON], --colorSpace, --auto
Space Type : --baseSpace, --colorSpace, --auto [ON]
Errors : --ignoreErrors, --printableErrors [100]
Errors : --ignoreErrors, --printableErrors [20]
The Validator Executable outputs error messages for invalid sequences based on [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]]. For Example:
The Validator Executable outputs error messages for invalid sequences based on [[C++ Class: FastQFile#Validation Criteria Used For Reading a Sequence|Validation Criteria]]. For Example:
There are a series of optional capabilities a FastQ Validator could implement. Among those:
There are a series of optional capabilities a FastQ Validator could implement. Among those:
*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
*To reduce memory usage, implement a two-pass algorithm that stores only a key for each sequence name (rather than complete sequence names) in memory (suggest a pair of options -1 -> one pass, high memory use, -2 -> two pass lower memory use, default is -1).
*Report average read quality score.
*Report average read quality score.
