FastQ Screen
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Application data |
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| Created by | Simon Andrews |
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| Biological application domain(s) | Genomics, Transcriptomics |
| Principal bioinformatics method(s) | Read mapping, Sequencing quality control |
| Technology | Illumina, ABI SOLiD |
| Created at | The Babraham Institute, Babraham Bioinformatics |
| Maintained? | Yes |
| Input format(s) | FASTQ |
| Output format(s) | Delimited Text, PNG |
| Software features | Summarises the mapping of a library against a series of reference sequences |
| Programming language(s) | Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux, Mac OS X, Windows |
Summary: FastQ Screen provides a simple way to screen a library of short reads against a set of reference libraries. Its most common use is as part of a QC pipeline to confirm that a library comes from the expected source, and to help identify any sources of contamination.
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Description
FastQ Screen is designed to be used as part of a QC pipeline and is a simple way to check that a sequence library contains the types of sequence expected.
The script is a wrapper around the bowtie aligner and provides a way to automate searches against a panel of bowtie libraries which could be the genomes of several different species, or common sources of contamination (Ecoli, Vectors, Adapters etc).
FastQ Screen collates the results of these searches and provides a summary in both text and graphical form which quickly allows you to see the distribution of hits against the various libraries searched.
The program has the option to extract a representative subset of sequences from the full library so searches can be completed quickly, and can identify sequences which map singly or multiple times, and those which are unique to a particular library vs those which could potentially map to more than one.
Links
References
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