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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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Versioning


No version available

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 citations

 (464)
call_split

Viromic Analysis of Wastewater Input to a River Catchment Reveals a Diverse Assemblage of RNA Viruses

2018
mSystems
PMCID: 5964442
DOI: 10.1128/mSystems.00025-18
call_split See protocol

[…] es were trimmed to remove Illumina adapters using Cutadapt version 1.2.1 with option -O 3 () and Sickle version 1.200 with a minimum quality score of 20 (). Further quality control was performed with Prinseq-lite () with the following parameters: minimum read length of 35, GC percentage between 5 and 95%, minimum mean quality of 25, dereplication (removal of identical reads, leaving 1 copy), and r […]

library_books

MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

2018
Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] ew England BioLabs) and sequenced on Illumina HiSeq 4000 using 50 bp single-read chemistry.Raw ChIP-seq reads were evaluated with FastQC (version 0.11.4). Quality-filtering and trimming was done with PRINSEQ-lite (version 0.20.4). Resulting high-quality reads were simultaneously mapped against the Mus musculus (GRCm38) and Drosophila melanogaster (dm6) reference genomes via BWA (version 0.7.15). S […]

call_split

The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

2018
Microbiome
PMCID: 5948730
PMID: 29753324
DOI: 10.1186/s40168-018-0477-5
call_split See protocol

[…] are deposited in the NCBI database within the Bioproject PRJNA380214 under the SRA study SRP133552.Prior to metagenomic analysis, sequence reads with a quality score mean below 30 were removed using Prinseq []. The 16S rRNA sequence analysis was performed using Mothur v. 1.39 []. Analysis was performed as according to the MiSeq SOP (accessed online 28/06/2017; []). The 16S rRNA gene sequences wer […]

call_split

Dissection of niche competition between introduced and indigenous arbuscular mycorrhizal fungi with respect to soybean yield responses

2018
Sci Rep
PMCID: 5943277
PMID: 29743529
DOI: 10.1038/s41598-018-25701-4
call_split See protocol

[…] gent Kit v3 (600 Cycles) (Illumina K.K., Tokyo).The nucleotides with a quality value (QV) <30 in the 3′ terminal and the adapter-index sequence in the 5′ terminal were trimmed from the MiSeq reads by PRINSEQ v0.20.4, and those shorter than 200 bp were excluded. After the quality filtering, an overlap fragment of the 300-bp-paired reads (read 1 and read 2) were constructed by using COPE v1.1.3 with […]

library_books

Gut microbiomes of wild great apes fluctuate seasonally in response to diet

2018
Nat Commun
PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] e genomes to remove host and any contaminant sequences. The de-multiplexed reads were trimmed to remove primers and adaptors and filtered to exclude short reads and those with low complexity regions (Prinseq v0.20.2, minimum quality mean = 30, max Ns = 20). A total of 512 million reads remained in the dataset after host subtraction and quality filtering (Average reads per sample = 27 million; rang […]

library_books

CLIP related methodologies and their application to retrovirology

2018
Retrovirology
PMCID: 5930818
PMID: 29716635
DOI: 10.1186/s12977-018-0417-2

[…] (http://hannonlab.cshl.edu/fastx_toolkit/), which provides a number of functions to accomplish all of these steps. Other alternatives, with more limited functions include Cutadapt [], Trimmomatic [], PRINSEQ [] as well as custom scripts.Mapping to reference genomes: The reads that pass the above filtering steps are mapped onto reference genomes or transcriptomes. The most commonly used mapping alg […]

Citations

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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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