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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 No




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Publication for Pyrocleaner

Pyrocleaner citations


Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella Specific trnD Gene Duplication

PLoS One
PMCID: 4866719
PMID: 27176910
DOI: 10.1371/journal.pone.0155441

[…] hei (454 flx+ and HiSeq2000) were generated as a by-product of a sequencing effort focused on the non-cultivable bacterial endosymbionts of these organisms []. In short, 454 reads were filtered using PyroCleaner v1.3 [] and the remaining reads were taxonomically assigned using PhymmBL v4.0 [] with custom-added genomes of representatives from the class Insecta (Atta cephalotes, Acyrthosiphon pisum, […]


Solving a Bloody Mess: B Vitamin Independent Metabolic Convergence among Gammaproteobacterial Obligate Endosymbionts from Blood Feeding Arthropods and the Leech Haementeria officinalis

Genome Biol Evol
PMCID: 4684696
PMID: 26454017
DOI: 10.1093/gbe/evv188
call_split See protocol

[…] accessed January 6, 2015). We discarded reads shorter than 100 bp, longer than 1,000 bp, those without a single base pair with quality higher than 35 and those with undefined nucleotides (“N”) using Pyrocleaner v1.3 (). The remaining reads were taxonomically assigned using PhymmBL v4.0 () with custom-added genomes of various representatives from the class Insecta (Atta cephalotes, Acyrthosiphon p […]


Comparative Genome Analyses Reveal Distinct Structure in the Saltwater Crocodile MHC

PLoS One
PMCID: 4263668
PMID: 25503521
DOI: 10.1371/journal.pone.0114631
call_split See protocol

[…] 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 platform, […]


The genome of the white rot fungus Pycnoporus cinnabarinus: a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown

BMC Genomics
PMCID: 4101180
PMID: 24942338
DOI: 10.1186/1471-2164-15-486

[…] ng of a 3 kbp paired-end genomic library using Illumina/Solexa Genome Analyzer II technology. The genomic Roche 454 read sets were uploaded to the ng6 storage environment []. Reads were cleaned using pyrocleaner [], which applied a low-complexity filter followed by a read-size filter (over 100 bp) and a duplication-removal filter. The 454 reads were then assembled using wgs-assembler version 6.0. […]


Transcriptome sequencing for high throughput SNP development and genetic mapping in Pea

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

[…] 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 […]


High density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

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

[…] 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 […]


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

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