Difference between revisions of "LibStatGen: FASTQ"
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| + | == Validation Criteria == | ||
| + | === Sequence Identifier Line === | ||
| + | *Every entry in the file should have a unique identifier. | ||
| + | |||
| + | === 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). | ||
| + | |||
| + | |||
| + | |||
| + | == Assumptions == | ||
| + | |||
== How to Use the fastQValidator Executable == | == How to Use the fastQValidator Executable == | ||
'''Required Parameters:''' | '''Required Parameters:''' | ||
| Line 22: | Line 52: | ||
== FastQ Validator Output == | == FastQ Validator Output == | ||
| − | + | '''Coming Soon''' | |
Revision as of 17:44, 3 February 2010
Validation Criteria
Sequence Identifier Line
- Every entry in the file should have a unique identifier.
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).
Assumptions
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.
Usage:
./fastQValidator -f <fileName> -l <minReadLen> -e <maxReprotedErrors> -b <rawSeqType>
Examples:
../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
