LibStatGen: FASTQ

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Revision as of 11:44, 4 February 2010 by Mktrost (talk | contribs) (Sequence Identifier Line)
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Validation Criteria

Sequence Identifier Line

Validation Criteria Error Message
Every entry in the file should have a unique identifier. ERROR on Line <current line #>: Repeated Sequence Identifier: <identifier> at Lines <previous line #> <current line #>

Raw Sequence Line

  • A base sequence should have non-zero length.
  • Validates the base sequences against the characters allowed via configuration.
    • Base Only: A C T G N a c t g n
    • Color Space Only: 0 1 2 3 .(period)
    • Base or Color Space: A C T G N a c t g n 0 1 2 3 .(period)
  • Reads should be of a minimum length; many mappers will get into trouble with very short reads.

Plus Line

Quality String Line

  • A quality string should be present for every base sequence.
  • Paired quality and base sequences should be of the same length.
  • Valid quality values should all have ASCII codes > 32.

Additional Features

  • Base composition are reported and tracked by position.
  • Consumes gzipped and uncompressed text files transparently (see libcsg/InputFile.h).

Additional Wishlist - Not Implemented

  • 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).


How to Use the fastQValidator Executable

Required Parameters:

       -f  :  FastQ filename with path to be prorcessed.

Optional Parameters:

       -l  :  Minimum allowed read length (Defaults to 10).
       -e  :  Maximum number of errors to display before suppressing them(Defaults to 20).
       -b  :  Raw sequence type:  B - ACTGN only (Default)
                                  C - 0123. only
                                 BC - ACTGN or 0123.

Testing only Parameters:

       -t  :  If "ReadOnly" is specified, the fastq will be read but not processed.  This may be used for determining read time.


       ./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>


       ../fastQValidator -f testFile.txt
       ../fastQValidator -f testFile.txt -l 10 -b BC -e 100
       ./fastQValidator -f test/testFile.txt -l 10 -b BC -e 100
       time ./fastQValidator -f test/testFile.txt -t ReadOnly

FastQ Validator Output

Coming Soon