FastQ Screen statistics

Tool stats & trends

Looking to identify usage trends or leading experts?


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




No version available



  • person_outline Simon Andrews
  • person_outline Steven Wingett

Additional information

FastQ Screen citations


Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

PLoS Genet
PMCID: 5882170
PMID: 29565971
DOI: 10.1371/journal.pgen.1007292

[…] clip ( To reduce any potential rRNA/total-RNA abundance biases introduced during rRNA depletion, reads mapping to rRNA genes were removed using FastQ Screen ( Reads were mapped to the WSM1271 genome (accession NC_014923) using Bowtie 2 [] and visualised using Artemis [] or Integrated Genome Browser [ […]


In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host Symbiont Interaction

PMCID: 5874924
PMID: 29559567
DOI: 10.1128/mBio.00024-18
call_split See protocol

[…] system at the University of Lausanne Genomic Technologies Facility. Purity-filtered reads were adapters and quality trimmed with Cutadapt v.1.8 (). Reads matching to rRNA sequences were removed with fastq_screen v. 0.9.3 (Babraham Bioinformatics; Remaining reads were further filtered for low complexity with reaper v. 15-065 (). Rea […]


Transcriptomic profiling of human breast and melanoma cells selected by migration through narrow constraints

Sci Data
PMCID: 5685158
PMID: 29135975
DOI: 10.1038/sdata.2017.172
call_split See protocol

[…] and alignment was carried out as described in reference. Quality control checks of raw RNA-Seq data files were done with fastqc v0.10.1 ( and fastq_screen v0.4.2 ( RNA-Seq reads were aligned to the human genome build GRCh38 with TopHat2.0.13 and genome annotation using GRCh38. […]


A Laboratory Methodology for Dual RNA Sequencing of Bacteria and their Host Cells In Vitro

Front Microbiol
PMCID: 5613115
PMID: 28983295
DOI: 10.3389/fmicb.2017.01830
call_split See protocol

[…] e that has been published previously (Marsh et al., ).Raw sequences are usually provided from the sequencing facility in FASTQ format, which can initially be subjected to contamination detection with FastQ Screen ( to ensure that the majority of reads are derived from the two organisms of interest. This is followed by an assessment of read q […]


High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

Sci Rep
PMCID: 5532269
PMID: 28751729
DOI: 10.1038/s41598-017-06110-5

[…] Library sequencing quality was determined using FastQC (Babraham Bioinformatics) and FastQ Screen (Babraham Bioinformatics). Illumina adaptor sequence and low quality read trimming (read pair removed if <20 base pairs) was performed using Trim Galore! (Babraham Bioinformatics: […]


Bromodomain Protein BRD4 Is a Transcriptional Repressor of Autophagy and Lysosomal Function

Mol Cell
PMCID: 5446411
PMID: 28525743
DOI: 10.1016/j.molcel.2017.04.027
call_split See protocol

[…] ds, single index). The results were then analyzed as follows. Quality checks on the raw RNA-Seq data files were conducted using fastqc ( and fastq_screen ( RNA-Seq reads were aligned to the GRCh37 () version of the human genome using tophat2 version 2.0.10 () with Bowtie vers […]


Looking to check out a full list of citations?

FastQ Screen review

star_border star_border star_border star_border star_border
star star star star star
Anamaria Elek's avatar image No country

Anamaria Elek

star_border star_border star_border star_border star_border
star star star star star
Does a pretty good job of mapping (subset of) your reads against different genomes, using aligner of your choice (Bowtie, Bowtie2 or BWA).