PRINSEQ protocols

PRINSEQ specifications

Information


Unique identifier OMICS_01068
Name PRINSEQ
Alternative name PReprocessing and INformation of SEQuences
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA,FASTQ
Biological technology Roche
Operating system Unix/Linux
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Maintained No

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Documentation


Maintainers


This tool is not maintained anymore.

Additional information


http://prinseq.sourceforge.net/manual.html

Information


Unique identifier OMICS_01068
Name PRINSEQ
Alternative name PReprocessing and INformation of SEQuences
Interface Web user interface
Restrictions to use None
Biological technology Roche
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Robert Edwards <>
  • person_outline Robert Schmieder <>

Additional information


http://prinseq.sourceforge.net/manual.html

Publication for PReprocessing and INformation of SEQuences

PRINSEQ IN pipelines

 (46)
2018
PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17

[…] an illumina miseq platform using a 250-bp paired-end format, resulting in a total of 5,320,190 reads. the raw sequences were preprocessed using cutadapt version 1.14 to trim adaptors (10) and using prinseq version 0.20.4 to perform quality filtering (11). initial genome assembly was performed with the spades version 3.10.0 genome assembler program (12). contigs less than 1,000 bp in length […]

2018
PMCID: 5795050
PMID: 29321239
DOI: 10.1098/rsob.170184

[…] illumina gaiix at the exeter sequencing service producing 2× 212 760 559 hiseq reads along with 2× 15 266 599 and 2× 16 274 715 gaiix reads. after trimming and cleaning (using tagcleaner [128] and prinseq [129]) of the data, we subsequently digitally normalized it with khmer [130] in order to discard redundant data and sampling variation and remove errors. this reduced the number of reads […]

2018
PMCID: 5805259
PMID: 29420668
DOI: 10.1371/journal.pone.0191867

[…] control of contamination., bioinformatic pre-processing of the viral metagenomes was performed as follows. fastq-format files containing raw sequence reads, were quality and length- filtered using prinseq-lite (v0.20.4) [18], which also implemented the removal of reads containing polynucleotide tails, ns and low complexity sequences. next, trimmed reads showing average quality below 20 […]

2018
PMCID: 5807056
PMID: 29290585
DOI: 10.1016/j.devcel.2017.12.005

[…] concentration of 1.5nm and sequenced on an illumina® nextseq 500 using 150bp paired end kit as per manufacturer’s instructions. see also key resources table., raw reads were initially processed with prinseq-lite v0.20.4 (schmieder and edwards, 2011) to trim low-quality reads. they were further aligned with tophat2 v2.0.11 (kim et al., 2013) on the grch37 human assembly and fpkm values […]

2018
PMCID: 5824556
PMID: 29471872
DOI: 10.1186/s40168-018-0424-5

[…] ultra-high-throughput sequencing system (illumina) using paired-ends (2 × 250 bp) for 500 cycles as per the manufacturers’ instructions., raw reads were quality-filtered, trimmed and screened using prinseq-lite v0.20.4 [29] in combination with in-house scripts. we used flash v1.2.11 (fast length adjustment of short reads) to align high-quality paired-end reads [30]. sequences were de novo […]

PRINSEQ institution(s)
Department of Computer Science, San Diego State University, San Diego, CA, USA; Computational Science Research Center, San Diego State University, San Diego, CA, USA; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA
PRINSEQ funding source(s)
Supported by Advances in Bioinformatics from the National Science Foundation (grant DBI 0850356).

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