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fqtools specifications


Unique identifier OMICS_11294
Name fqtools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format FASTQ
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Alastair Droop

Publication for fqtools

fqtools citations


In vivo loss of carbapenem resistance by extensively drug resistant Klebsiella pneumoniae during treatment via porin expression modification

Sci Rep
PMCID: 5532282
PMID: 28751669
DOI: 10.1038/s41598-017-06503-6

[…] all reads were processed to remove low quality or artefactual nucleotides, using sequentially sickle (github.com/najoshi/sickle), alientrimmer, and fqduplicate (ftp.pasteur.fr/pub/gensoft/projects/fqtools). read pairs were assembled using clc assembler from the clc genomics workbench analysis package (www.clcbio.com/products/clc-genomics-workbench). all contigs of ≥500 nt were reordered […]


Multicenter Outbreak of Infections by Saprochaete clavata, an Unrecognized Opportunistic Fungal Pathogen

PMCID: 4271555
PMID: 25516620
DOI: 10.1128/mBio.02309-14
call_split See protocol

[…] above were discarded, as were those containing more than 5% of the remaining nucleotides with a phred score of <28. finally, the program fqduplicate (http://ftp.pasteur.fr/pub/gensoft/projects/fqtools) was used to discard every duplicate single- or paired-end read., whole-genome de novo assembly for each strain was performed using the program clc_novo_assemble (clc bio, aarhus, denmark). […]


Draft Genome Sequence of Campylobacter coli Strain IPSID 1 Isolated from a Patient with Immunoproliferative Small Intestinal Disease

Genome Announc
PMCID: 3953186
PMID: 24625865
DOI: 10.1128/genomeA.00079-14

[…] t;95 bp after the above cleaning steps were discarded, as well as those containing >20% bp with a phred score of <20. finally, the program fqduplicate (ftp://ftp.pasteur.fr/pub/gensoft/projects/fqtools) was used to discard every duplicate paired-end read. the remaining reads (~6,682,000 paired-end and ~2,176,000 single-end) were assembled using clc_assembler (version 4.10.86742) from the clc […]

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fqtools institution(s)
MRC Medical Bioinformatics Centre, University of Leeds, Leeds, UK
fqtools funding source(s)
This work has been supported by the Leeds MRC Medical Bioinformatics Centre [MR/LO1629X] and the Cancer Research UK Leeds Centre [infrastructure award C37059/A18080].

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