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 Yes

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PEAR article

PEAR citations

 (5)
2018
PMCID: 5827094

[…] libraries were sequenced using the illumina miseq platform (illumina) and the miseq reagent kit v3 (600 cycles) (illumina)., for the shotgun metagenomic dataset, overlapping reads were paired using pear 0.9.5 (zhang et al., 2014) and filtered for quality with phred > 30, and a length longer than 80 nt using seqyclean 1.9.81. the reads were annotated by blastx against the ncbi-nr database […]

2016
PMCID: 5156904

[…] the effect size and associated confidence interval for each function detected to be of significance biological relevance (t-test, p-value < 0.05) were generated (supplementary fig. s2)., using pear77, metagenomic datasets were merged (r1 and r2) and the leftover (not merged) reads from r1 included within the output. sequences below 50 nucleotides length and q20 were removed. the screening […]

2016
PMCID: 5144678

[…] reads with both paired-end reads available were used for further analysis. the bam-files were first converted to fastq format using bamtools,48 and only reads with both paired-ends were merged using pear.49 after merging, the forward and reverse mapping reads were again separately mapped to the sample-specific reference sequence using bwa50 for the further independent analysis of forward […]

2015
PMCID: 4408351

[…] usa). whole-genome sequencing was performed with the miseq platform (illumina, usa) using the 600-cycle miseq reagent kit v3 (illumina). initially, the obtained paired reads were merged with pear 0.9.5 (4). bases with quality scores under phred 30 and sequences shorter than 50 bp were removed with seqyclean 1.9.8 (https://bitbucket.org/izhbannikov/seqyclean). de novo genome assembly […]

2015
PMCID: 4442144

[…] 400 nt; therefore, paired-end miseq 250 nt reads contained overlapping 3′ sequences. using these overlapping sequences, paired reads were combined into one sequence using the paired-end assembler (pear, v. 0.8.1) and default options (zhang et al., 2014). an index of all possible dscam1 ligamer combinations was created using a single perl script that permuted all possible ligamer combinations […]

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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