PRINSEQ protocols

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PRINSEQ specifications


Unique identifier OMICS_01068
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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Additional information


Unique identifier OMICS_01068
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



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

Additional information

Publication for PReprocessing and INformation of SEQuences

PRINSEQ in pipelines

PMCID: 5754489
PMID: 29301880
DOI: 10.1128/genomeA.01399-17

[…] on 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 () and using prinseq version 0.20.4 to perform quality filtering (). initial genome assembly was performed with the spades version 3.10.0 genome assembler program (). contigs less than 1,000 bp in length […]

PMCID: 5790269
PMID: 29381713
DOI: 10.1371/journal.pone.0191650

[…] information using the silva database []. the steps for data processing and assignment were as follows: (i) trimming sequences with a quality score from the 3'-end with a threshold score of 20 in prinseq []; (ii) removing reads of the phix genome with bowtie2 []; (iii) trimming primer sequences at a 20% error tolerance in cutadapt []; (iv) joining paired-end reads with qiime []; (v) filtering […]

PMCID: 5794742
PMID: 29391533
DOI: 10.1038/s41598-018-20358-5

[…] reporter v2.6 or bcl2fastq v2.17., a bioinformatics pipeline was developed to analyze the ngs data to determine indel and hdr frequencies. quality filtering was performed on paired-end reads using prinseq. reads with quality score mean below 30 or length shorter than 50 were removed. the remaining reads were then aligned to a reference genome with bwa, followed by realignment using abra […]

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

[…] bp) 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 [] and prinseq []) of the data, we subsequently digitally normalized it with khmer [] in order to discard redundant data and sampling variation and remove errors. this reduced the number of reads to 415 241 […]

PMCID: 5798017
PMID: 29360959
DOI: 10.1093/gbe/evy015

[…] (project accession: prjna385897)., a de novo transcriptome assembly for a. svalbardicum was obtained following the methods of . low quality parts of the reads were trimmed from the right ends with prinseq-lite (; last accessed january 25, 2017) when the mean of phred score in a 20-bp window was <20. reads longer than 20 bp after trimming were reorganized […]

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PRINSEQ in publications

PMCID: 5964442
DOI: 10.1128/mSystems.00025-18

[…] 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), […]

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

[…] 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). […]

PMCID: 5948730
PMID: 29753324
DOI: 10.1186/s40168-018-0477-5

[…] 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 […]

PMCID: 5943277
PMID: 29743529
DOI: 10.1038/s41598-018-25701-4

[…] 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 […]

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

[…] 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; […]

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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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