QTrim protocols

QTrim specifications

Information


Unique identifier OMICS_01089
Name QTrim
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data High throughput sequence data
Input format FASTQ, FASTA + QUAL
Output data High quality reads
Output format FASTQ, FASTA + QUAL
Biological technology Roche
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements BioPython, Numpy, Matplotlib
Maintained Yes

Versioning


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Maintainer


  • person_outline Simon A. Travers <>

Information


Unique identifier OMICS_01089
Name QTrim
Interface Web user interface
Restrictions to use None
Input data High throughput sequence data
Input format FASTQ, FASTA + QUAL
Output data High quality reads
Output format FASTQ, FASTA + QUAL
Programming languages Python
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Simon A. Travers <>

Publication for QTrim

QTrim IN pipelines

 (3)
2018
PMCID: 5871332
PMID: 29582753
DOI: 10.7554/eLife.33014.035

[…] depth of 800x. sequence quality was examined using fastqc (rrid:scr_014583, http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) and sequence reads were quality trimmed (parameters: minlen = 50 qtrim = rl trimq = 15 ktrim = r k = 21 mink = 8 ref=$adapters hdist = 2 hdist2 = 1 tbo = t tpe = t) and cleared of human (parameters: minid = 0.95 maxindel = 3 bwr = 0.16 bw = 12 quickmatch fast […]

2018
PMCID: 5871332
PMID: 29582753
DOI: 10.7554/eLife.33014.035

[…] rl trimq = 15 ktrim = r k = 21 mink = 8 ref=$adapters hdist = 2 hdist2 = 1 tbo = t tpe = t) and cleared of human (parameters: minid = 0.95 maxindel = 3 bwr = 0.16 bw = 12 quickmatch fast minhits = 2 qtrim = lr trimq = 10) and phix (parameters: k = 31 hdist = 1) sequences against the whole respective genomes using bbmap v35 (http://sourceforge.net/projects/bbmap/)., for pacbio sequencing, bsv […]

2016
PMCID: 5146979
PMID: 28018369
DOI: 10.3389/fpls.2016.01793

[…] inc., san diego, ca, usa). samples were sequenced twice in separated lanes. paired-end (2 × 100 bp) and raw reads were pre-processed for quality using fastqc 0.11.21 and adapter trimming with qtrim v0.942. the resulting pre-processed reads were aligned to the reference transcriptome of vitis vinifera (v1 grapevine annotation)3 using the bowtie2 aligner v2.2.3 (langmead and salzberg, 2012) […]

QTrim institution(s)
South African National Bioinformatics Institute, SA MRC Bioinformatics Unit, University of the Western Cape, Bellville, South Africa; Ryan Institute, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland; Retroviruses and Molecular Evolution, CNRS-UPR 9002, Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France; School of Life Sciences, University of Warwick, Coventry, UK
QTrim funding source(s)
This work was supported by a student bursary from Atlantic Philanthropies (grant # 62302) and by an award from the South African Department of Science and Technology. This work was further supported by Science Foundation Ireland (grant n°07/RFP/EEEOBF424).

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