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PEAR specifications

Information


Unique identifier OMICS_00674
Name PEAR
Alternative name Paired-End reAd mergeR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 0.9.8
Stability Stable
Maintained No

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Publication for Paired-End reAd mergeR

PEAR citations

 (194)
call_split

Networks of genetic similarity reveal non neutral processes shape strain structure in Plasmodium falciparum

2018
Nat Commun
PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3
call_split See protocol

[…] identifier (MID) tags in the forward and reverse reads. A minimum read length of 100nt and a maximum uncalled bases threshold of 15 were used. The resulting paired fastq files were then merged using PEAR v.0.9.10, to ensure the resulting merged fastq files had appropriate base quality scores allowing for filtering of low quality reads. The minimum assembly length was set to 100nt and the minimum […]

call_split

Effect of PEAR1 Genetic Variants on 1 Year Outcomes in Chinese Patients with Acute Myocardial Infarction After Percutaneous Coronary Intervention

2018
PMCID: 5945558
PMID: 29212986
DOI: 10.5551/jat.39982
call_split See protocol

[…] tegorical variables were reported as counts (percentages) and Chi-square test (χ2) was used to compare groups. Multivariate stepwise Cox regression analysis was conducted to identify independent risk PEAR1-SNPs related to adverse ischemic events after adjusting for potential confounders which may affect outcomes including age, sex, BMI, DM, hypertension, hypercholesterolemia, smoking, alcohol, pla […]

library_books

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces

2018
Sci Data
PMCID: 5914283
PMID: 29688220
DOI: 10.1038/sdata.2018.68

[…] using BWA (ver. 0.7.15). From the BAM-formatted aligned file, the aligned reads were selected using an in-house script that was designed to screen out unmapped reads. The reads were then joined using PEAR, with default parameters. Reads shorter than 200 bp were excluded from downstream analysis. […]

library_books

Metabarcoding analysis of strongylid nematode diversity in two sympatric primate species

2018
Sci Rep
PMCID: 5897349
PMID: 29651122
DOI: 10.1038/s41598-018-24126-3

[…] ive (project accession no.: PRJEB21189). Sample metadata along with sample accession numbers are given in Table . We demultiplexed resulting fastq files using skewer and assembled paired-end reads by pear. Subsequently, using dada2 we eliminated sequences, where the expected number of sequencing errors was higher than one and performed denoising on the filtered dataset to estimate relative abundan […]

library_books

Fermentation products in the cystic fibrosis airways induce aggregation and dormancy associated expression profiles in a CF clinical isolate of Pseudomonas aeruginosa

2018
FEMS Microbiol Lett
PMCID: 5928460
PMID: 29617986
DOI: 10.1093/femsle/fny082

[…] Quality control and filtering of transcriptome data were performed with Trimmomatic, PEAR (Paired-End reAd mergeR) and Deconseq. Trimmomatic trimmed adapter sequences, low-quality reads and removed Ns (Bolger, Lohse and Usadel ). PEAR combined overlapping paired reads into a single re […]

call_split

Behaviour during transportation predicts stress response and lower airway contamination in horses

2018
PLoS One
PMCID: 5863983
PMID: 29566072
DOI: 10.1371/journal.pone.0194272
call_split See protocol

[…] was then measured by qPCR and sequenced (Illumina MiSeq; San Diego, CA, USA) with 2 x 300 base pairs paired-end chemistry. Paired-end reads were assembled by aligning forward and reverse reads using PEAR (version 0.9.5) []. Primers were trimmed using Seqtk (version 1.0) [] and trimmed sequences were processed using Quantitative Insights into Microbial Ecology (QIIME 1.8) [] USEARCH (version 8.0.1 […]

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PEAR institution(s)
The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Graduate School for Computing in Medicine and Life Sciences, Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany; Karlsruhe Institute of Technology, Institute for Theoretical Informatics, Karlsruhe, Germany
PEAR funding source(s)
Supported by a HITS scholarship, the DFG project STA-860/4 and the Graduate School for Computing in Medicine and Life Sciences, University of Lubeck.

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