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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.
Language Perl
Requirements Linux-based operating system
Bowtie or Bowtie2 or BWA
gzip (optional)
SAMtools (optional)
GD::Graph (optional)
Bismark (bisulfite mapping only)
Code Maturity Stable - has been working in production for some time
Code Released Yes, under GPL v3 or later.
Documention Online documentation here
Online Tutorials Online tutorials here
Initial Contact Steven Wingett

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FastQ Screen Logo

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.

Click here for a video introduction to FastQ Screen.

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:

A good screen result

..and not bad, like this:

A bad screen result