FastQ Screen protocols

FastQ Screen computational protocol

FastQ Screen specifications


Unique identifier OMICS_01042
Name FastQ Screen
Alternative name fastq_screen
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data Text based and graphical output which summaries the mapping of the sequences against each library.
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 0.11.4
Stability Stable
Bowtie, Bismark
Maintained Yes



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  • person_outline Simon Andrews <>
  • person_outline Steven Wingett <>

Additional information

FastQ Screen IN pipeline

PMCID: 4428251
PMID: 25969736
DOI: 10.1186/s40168-015-0083-8

[…] of non-bacterial dna in the adenoid biopsies. we note there are a variety of stand-alone methods available to eliminate this type of non-bacterial signal, such as deconseq [12], kraken [11] and fastq screen (babraham bioinformatics, babraham institute, uk). however, by utilising parameters in qiime, we were able to achieve an efficient removal of the non-bacterial signal within the qiime […]

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