Pyrocleaner protocols

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Pyrocleaner specifications


Unique identifier OMICS_01069
Name Pyrocleaner
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The list of files to clean or the single file to clean.
Input format SFF,FASTQ,FASTA
Output format SFF,FASTQ,FASTA
Biological technology Roche
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Jérôme Mariette <>

Publication for Pyrocleaner

Pyrocleaner in pipelines

PMCID: 3639946
PMID: 23575249
DOI: 10.1186/1471-2164-14-236

[…] to each contig for each library were indicative of the level of gene expression. we corrected for artificial duplication biases during emulsion pcr, by developing an in-house tool called ‘pyrocleaner’ []. we defined duplicated reads as clusters in megablast [] analyses with a minimum hit score of 100, a percent identity cutoff of 98, with an alignment of reads starting at exactly […]

PMCID: 4046650
PMID: 24261852
DOI: 10.1186/1471-2164-14-814

[…] full bac sequencing was performed using 454 multiplexing technology on a gs-flx titanium sequencer (454 life sciences, roche diagnostics, branford, connecticut, usa). raw reads were cleaned using pyrocleaner []. reads sharing more than 95% homology with bac vector or escherichia coli genome sequence were excluded. de novo assembly of the cleaned reads was performed using newbler (version 2.3; […]

Pyrocleaner in publications

PMCID: 5281569
PMID: 28197152
DOI: 10.3389/fpls.2016.02034

[…] sequence data assembly was performed with newbler 2.8 software sold by 454 life sciences/roche for 454 data (veras et al., ). the assembly was performed on data previously processed by the software pyrocleaner after clearing reads from contamination by the host e. coli. sequenced bac dna was analyzed using triannot pipeline v.3.8 improved for wheat species […]

PMCID: 4263668
PMID: 25503521
DOI: 10.1371/journal.pone.0114631

[…] for the 454 sequencing system ( was conducted., quality control of the raw 454 reads from each bac was performed using the following three steps: i) removal of duplicated reads (pyrocleaner), ii) trimming of adapter and low quality sequences (sff_extract), and iii) filtering by read size. the pyrocleaner was used to remove duplicated reads generated by the roche 454 […]

PMCID: 4210547
PMID: 25325924
DOI: 10.1186/s12870-014-0279-2

[…] science corp., brandford, connecticut, usa) were performed at genotoul genomic (, inra toulouse, france)., checking for contaminants and quality trimming was performed using pyrocleaner software suite []. assembly and polymorphism discovery were performed using ngen® version 3 (dnastar, madison, wi, usa) []. reads were mapped on the reference genome v2.4 […]

PMCID: 3925251
PMID: 24521263
DOI: 10.1186/1471-2164-15-126

[…] 400 mb sequences (1 million reads, 400 pb length), was necessary to sequence the eight cultivars. raw data were produced as sff files., raw data were first processed through different cleaning steps. pyrocleaner v1.0 [] was used to remove sequences with a length outside a given range (mean read length +/− 2 × standard deviation), as well as potential pcr duplicates, and low complexity sequences. r […]

PMCID: 3660193
PMID: 23597128
DOI: 10.1186/1741-7007-11-50

[…] in additional file ) were recovered from the ncbi dbest and genbank databases., all 454 reads were produced with the smart pcr cdna synthesis kit. data were cleaned with the smartkitcleaner and pyrocleaner tools [], based on the following steps: i) clipping of adaptors with cross_match []; ii) removal of reads outside of the length range (150 to 600); iii) removal of reads with a percentage […]

Pyrocleaner institution(s)
Plate-forme bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle/Génétique Cellulaire, France

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