3,045
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchno edit summary
This command line tool can be found at: http://www.sph.umich.edu/csg/mktrost/fastQFile/
This command line tool can be found at: http://www.sph.umich.edu/csg/mktrost/fastQFile/
Note: Since the FastQValidator checks for unique sequence names, it may use a large amount of memory.
== Valid FastQ File Requirements ==
== Valid FastQ File Requirements ==
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:
*Add option to disable the unique sequence name validation so it does not store all the sequence names.
*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.
