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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Versioning


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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

PRINSEQ article

PRINSEQ citations

 (17)
2018
PMCID: 5920166

[…] ipswich, ma), following the manufacturer’s instructions, and sequenced in a 2 × 300 pair-end sequencing run on a miseq sequencer (illumina, san diego, ca)., raw reads were quality trimmed with prinseq lite v0.20.4 (4). the resulting 5,830,860 pairs were processed with the squeezem pipeline (j. tamames, unpublished data). briefly, they were assembled using megahit v1.1.2 (5), and open […]

2018
PMCID: 5824556

[…] 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 […]

2018
PMCID: 5805259

[…] 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 […]

2017
PMCID: 5559432

[…] mrna sample preparation, illumina) and paired-end sequencing (miseq, 2 × 300 bp) were performed at fasteris (plan-les-ouates, switzerland)., the paired-end sequences were assessed for quality with prinseq (schmieder and edwards, 2011) and joined with fastq-join from the ea-utils software package (aronesty, 2013), and the rrna sequences were removed from the data set using sortmerna (v. 2.0) […]

2017
PMCID: 5546698

[…] using the truseq chip library preparation kits and hiseq2000 sequencer. read length was 100bp., to ensure the use of high quality reads, raw reads from the illumina sequencer were filtered using prinseq [49]. only reads with phred score above 25 for every base were used for the downstream analysis. reads that matched t0 reads were removed from the other time points (t6, t24) using cd-hit […]

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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