PEAR protocols

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PEAR specifications

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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 in pipelines

 (69)
2018
PMCID: 5762663
PMID: 29321528
DOI: 10.1038/s41467-017-02535-8

[…] in a local cluster [marbits platform, icm] (logares). briefly, raw reads were corrected using bayeshammer following schirmer et al.. corrected paired-end reads were subsequently merged with pear; sequences longer than 200 bp were quality-checked (maximum expected errors 0.5) and de-replicated using usearch. otu were delineated at 97% similarity using uparse v8.1.1756. to obtain otu […]

2018
PMCID: 5768916
PMID: 29375529
DOI: 10.3389/fmicb.2017.02667

[…] of sequence reads was largely completed following the pipeline developed by . paired-end reads were assembled by aligning the forward and reverse reads by their common overlapping parts using pear (version 0.9.1) (). 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 sequences […]

2018
PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] remaining (20 cn and 18 cd). a mean of 21,793 raw pe read pairs were produced over these remaining samples (min = 9503; max = 40,392). forward and reverse reads were then stitched together using pear [] (v0.9.6) with an assembly rate > 80% for all samples except for sample s22 (68.7% of reads assembled). we then filtered out stitched reads with a quality score < 30 over 90% of bases […]

2018
PMCID: 5780513
PMID: 29362388
DOI: 10.1038/s41598-018-19743-x

[…] (2 × 300 bp) with v3 chemistry for the illumina miseq platform., demultiplexing of raw sequences was performed by casava data analysis software (illumina). paired-end sequences were merged using pear v0.9.10 (64 bit) with default parameters. sequences with average quality score lower than 20 or containing unresolved nucleotides were removed from the dataset with the split_libraries_fastq.py […]

2018
PMCID: 5792456
PMID: 29386569
DOI: 10.1038/s41598-018-20393-2

[…] 16s ssu rrna gene using illumina miseq. 2 × 300 paired end sequencing by stab vida sequencing services (portugal). raw data was processed in qiime 1.9.1. first, paired end reads were assembled using pear. quality control and trimming were performed using fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and bbduk (minlength = 75 trimq = 20; […]


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PEAR in publications

 (186)
PMCID: 5940794
PMID: 29739937
DOI: 10.1038/s41467-018-04219-3

[…] 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 […]

PMCID: 5923270
PMID: 29703936
DOI: 10.1038/s41598-018-25190-5

[…] (uic). sequencing was performed at the w.m. keck center for comparative and functional genomics at the university of illinois at urbana-champaign (uiuc)., forward and reverse reads were merged using pear. primer sequences were identified using smith-watermann alignment and trimmed from the sequence. reads that lacked either primer sequence were discarded. sequences were then trimmed based […]

PMCID: 5919928
PMID: 29700429
DOI: 10.1038/s41598-018-25079-3

[…] stab vida lda. (caparica, portugal). raw data derived from fungal its genes illumina run were processed according to the following pipeline. paired-end reads from each library were paired via pear. sequences with a quality score threshold lower than 30 and shorter than 150 bp were discarded. assembled reads were analyzed via qiime v.1.8 software package. sequences were checked […]

PMCID: 5914283
PMID: 29688220
DOI: 10.1038/sdata.2018.68

[…] trimming options. reads that passed the filtering process for both paired reads were used for downstream analysis. the filtered paired-end reads were joined into single-sequence reads using the paired-end read merger pear (ver. 0.9.8) and default parameters. to exclude anomalously joined reads, reads that were too short or too long were excluded according to the expected size […]

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

[…] (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 […]


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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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