PEAR pipeline

PEAR specifications


Unique identifier OMICS_00674
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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Publication for Paired-End reAd mergeR

PEAR citations

PMCID: 5768916

[…] was largely completed following the pipeline developed by comeau et al. (2017). paired-end reads were assembled by aligning the forward and reverse reads by their common overlapping parts using pear (version 0.9.1) (zhang et al., 2014). quality metrics were checked using fastqc (version 0.11.5) and filtered using tools in fastx (version 0.7) and bbmap (version 35.84). ambiguous and chimeric […]

PMCID: 5557836

[…] pca was performed using program eigensoft34. a neighbor-joining phylogenetic tree was constructed using mega635 in 1000 bootstrap replicates with pear “pyrus × bretschneideri” as the outgroup. pear genomic sequence reads36 were downloaded from the ncbi sra database (accession no. srp016889) and aligned to the apple genome v1.0p for snp calling. population structure was investigated using […]

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 […]

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 […]

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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