PyroTrimmer protocols

View PyroTrimmer computational protocol

PyroTrimmer statistics

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PyroTrimmer specifications

Information


Unique identifier OMICS_11157
Name PyroTrimmer
Software type Application/Script
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data PyroTrimmer takes tag, fasta and quality file as input. Tag file include project, names of genes and samples, upper or lower length cutoffs of reads, and sequences of barcodes-linkers-primers.
Biological technology Roche
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Kyung Mo Kim <>

Publication for PyroTrimmer

PyroTrimmer in pipelines

 (2)
2016
PMCID: 5013075
PMID: 27656163
DOI: 10.3389/fmicb.2016.01314

[…] ct, usa) at omicspia, co. ltd., amplicon reads of the partial 16s ribosomal rna genes (v1–v3 regions) generated by the 454 gs flx titanium platform were initially trimmed for quality using the pyrotrimmer program v1.1 (). bacterial 16s rrna sequence data from the microbiota in the rhizosphere of pepper plants were processed through the mothur pipeline (). reads were sorted into each sample […]

2015
PMCID: 4370865
PMID: 25799273
DOI: 10.1371/journal.pone.0119966

[…] product. 16s amplicon sequencing was performed by dnalink inc. (seoul, korea) using the 454 gs flx titanium sequencing system (roche 454 life sciences, usa). raw reads were initially processed using pyrotrimmer, which attempts to trim barcode, linker, and primer sequences and filter out low-quality sequences based on read length, homopolymers, and quality score []. the resultant sequences […]


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PyroTrimmer in publications

 (2)
PMCID: 5450337
PMID: 28558648
DOI: 10.1186/s12862-017-0966-3

[…] : table s1, barcodes in additional file : table s2a). amplicons from 45 independent reactions were pooled and sequenced using 454 gs-flx titanium sequencing machine (roche, branford, ct). we used pyrotrimmer [] to remove the barcode, linker and primer sequences, and trim the 3′-ends of sequences with low-quality reads (i.e. average score < 20 nucleotides per 5-bp sliding window). ambiguous […]

PMCID: 5013075
PMID: 27656163
DOI: 10.3389/fmicb.2016.01314

[…] ct, usa) at omicspia, co. ltd., amplicon reads of the partial 16s ribosomal rna genes (v1–v3 regions) generated by the 454 gs flx titanium platform were initially trimmed for quality using the pyrotrimmer program v1.1 (). bacterial 16s rrna sequence data from the microbiota in the rhizosphere of pepper plants were processed through the mothur pipeline (). reads were sorted into each sample […]


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PyroTrimmer institution(s)
Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea; Department of Bio-Information Technology, Chungbuk National University, CheongJu, Korea; Department of Systems Biology, Yonsei University, Seoul, Korea; Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, Korea

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