FastQ Screen
| Function | FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. |
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| Language | Perl |
| Requirements | Bowtie and GD::Graph |
| Code Maturity | Beta - working, but feedback is appreciated |
| Code Released | Yes, under GPL v3 or later. |
| Initial Contact | Simon Andrews |
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When running a sequencing pipeline it is useful to know that your sequencing runs contain the types of sequence they're supposed to.
FastQ Screen allows you to set up a standard set of libraries against which all of your sequences can be searched. Your search libraries might contain the genomes of all of the organisms you work on, along with PhiX, Vectors or other contaminants commonly seen in sequencing experiments.
The program produces both text based and graphical output which summaries the mapping of your sequences against each of your libraries, so that when you search your mouse sequences you can see if they're good, like this:
..and not bad, like this:
Changelog
- 18-4-12: Version 0.3.1 released
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- Fixed bug preventing use of the Bowtie argument (--bowtie, -b)
- 29-3-12: Version 0.3 released
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- The --multilib option was removed. This script now returns simultaneously all the information previously obtained by selecting/not selecting --multilib
- Added --nohits option which prints to an output file sequence reads or read pairs that mapped to none of the reference genomes
- Option --illumina flag has changed to --illumina1_3
- Script can process files compressed with gzip
- 19-5-11: Version 0.2.1 released
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- Fixed a bug in multilib paired end searches which caused reported mapped percentages to be double the true value
- 18-5-11: Version 0.2 released
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- Added --multilib option for better comparisons between genomes
- Added colorspace support
- Allow override of default config file
- 24-03-11: Version 0.1 released