- 1 Status
- 2 Valid FastQ File Requirements
- 3 How to Use the fastQValidator Executable
- 4 FastQ Validator Output
- 5 Libraries & Classes
- 6 Additional Features
- 7 Additional Wishlist - Not Implemented
- 8 Discussion
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.
Valid FastQ File Requirements
A valid fastQ file meets the validation criteria specified in FastQ Validation Criteria.
How to Use the fastQValidator Executable
--file : FastQ filename with path to be processed.
--minReadLen : Minimum allowed read length (Defaults to 10). --maxErrors : Number of errors to allow before quitting reading/validating the file. -1 (default) indicates to not quit until the entire file is read. 0 indicates not to read/validate anything --printableErrors : Maximum number of errors to print before suppressing them (Defaults to 20). Different than maxErrors since printableErrors will continue reading and validating the file until the end, but just doesn't print the errors. --ignoreErrors : Ignore all errors (same as printableErrors = 0) overwrites the printableErrors option. --baseComposition : Print the Base Composition Statistics. --quiet : Suppresses the display of errors and summary statistics. Does not affect the printing of Base Composition Statistics.
Optional Space Options for Raw Sequence (Last one specified is used)
--auto : Determine baseSpace/colorSpace from the Raw Sequence in the file (Default). --baseSpace : ACTGN only --colorSpace : 0123. only (with 1 character primer base)
./fastQValidator --file <fileName> [--minReadLen <minReadLen>] [--maxErrors <numErrors>] [--printableErrors <printableErrors>|--ignoreErrors] [--baseSpace|--colorSpace|--auto] [--baseComposition] [--quiet]
./fastQValidator --file testFile.txt ./fastQValidator --file testFile.txt --minReadLen 10 --baseSpace --printableErrors 100 ./fastQValidator --file test/testFile.txt --minReadLen 10 --colorSpace --ignoreErrors
- 0 - the fastq file is valid.
- < 0 - invalid options specified.
- > 0 - fastq file did not validate succesfully. One of the FastQStatus failure values is returned
FastQ Validator Output
When running the fastQValidator Executable, the output starts with a summary of the parameters:
The following parameters are in effect:
Input Parameters --file [testFile.txt], --baseComposition [ON], --quiet, --minReadLen , --maxErrors [-1] Space Type : --baseSpace [ON], --colorSpace, --auto Errors : --ignoreErrors, --printableErrors 
The Validator Executable outputs error messages for invalid sequences based on Validation Criteria. For Example:
ERROR on Line 25: The sequence identifier line was too short. ERROR on Line 29: First line of a sequence does not begin wtih @ ERROR on Line 33: No Sequence Identifier specified before the comment.
Base Composition Percentages by Index are printed if --printBaseComp is set to ON. For Example:
Base Composition Statistics: Read Index %A %C %G %T %N Total Reads At Index 0 100.00 0.00 0.00 0.00 0.00 20 1 5.00 95.00 0.00 0.00 0.00 20 2 5.00 0.00 5.00 90.00 0.00 20
Summary of the number of lines, sequences, and errors:
Finished processing testFile.txt with 92 lines containing 20 sequences. There were a total of 17 errors.
Libraries & Classes
- C++ Library: libStatGen
- ParameterList - Class for reading in Parameters.
- FastQValidator.cpp - Main method for the Executable.
- Base composition reported and tracked by position.
- Supports base space and color space files.
- Consumes gzipped and uncompressed text files transparently.
- Prints error messages for errors up to the configurable maximum number of reportable errors.
- Prints a summary of the total number of errors.
- Prints the total number of lines processed as well as the total number of sequences processed.
Additional Wishlist - Not Implemented
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).
- Report average read quality score.
- AutoDetect 64/33 illumina/standard quality scores.
- For color space, there is no specification for:
- The length of read and quality string may be the same or differs by 1 (depending on whether the primer base has a corresponding quality value).
- Decided to require a quality score for the primer base.
- Missing values are usually presented by "." or sometimes left as a blank " ".
- Tag names for paired end reads may be the same (e.g. MAQ actually enforces that), and may be in the same file (e.g. BFAST require paired reads in the same file)
- It may be useful to report 2 types of information to the user: ERROR (critical failure) and WARNING (tolerable errors).