PyroBayes protocols

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PyroBayes specifications

Information


Unique identifier OMICS_01155
Name PyroBayes
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Roche
Operating system Unix/Linux
Computer skills Advanced
Version 0.9
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Aaron Quinlan <>
  • person_outline Gabor Marth <>

Publication for PyroBayes

PyroBayes in pipelines

 (9)
2015
PMCID: 4403768
PMID: 25887695
DOI: 10.1186/s12866-015-0388-6

[…] to allow multiplexing of samples in a sequencing pool. pyrosequencing was performed using a roche/454 flx genome sequencer according to the manufacturer’s instructions. sequences were analysed using pyrobayes [], pintail chimera detection algorithm [] and qiime v1.6.0 []. sequences were quality trimmed as described previously []. otu picking was done at 3% divergence level, de-noising […]

2014
PMCID: 4060450
PMID: 24886912
DOI: 10.1186/ar4566

[…] in the 454 data. capillary sequencing of these amplicons used the 3730xl platform (applied biosystems, ca, usa)., the 454 sequence read demultiplexing used ”untag” software []; base calling used pyrobayes []; and alignment to the reference genome used bwa []. variant calling was carried out by using gatk [] without duplicate read removal, by using hard filters: coverage at least 10-fold; […]

2014
PMCID: 4148237
PMID: 25167074
DOI: 10.1371/journal.pone.0104739

[…] to amplify the v1 to v3 region of the 16s rrna gene. sequencing was performed on a roche/454 flx+ genome sequencer according to manufacturer’s instructions. the data pre-processing was done using pyrobayes followed by further analysis in qiime v1.6.0 using usearch, uchime and uclust algorithms at sequence similarity threshold of 97% and blast taxonomy assignments. sequences were trimmed […]

2013
PMCID: 3616924
PMID: 23593027
DOI: 10.1371/journal.pgen.1003429

[…] to ft and non-ft regions are listed in and ., raw data in sff format were obtained using a 454 roche gs flx life sciences pyrosequencing machine. data were then decoded to fastq/fasta format using pyrobayes (http://bioinformatics.bc.edu/marthlab/pyrobayes). elimination of primers sequences was performed by perl script using bioperl as interface to fasta, with the assumption that a primer […]

2013
PMCID: 3731364
PMID: 23936375
DOI: 10.1371/journal.pone.0070051

[…] all hiseq2000 sequence data have been submitted to the ncbi sequence read archive (sra) under the bioproject accession number prjna202430., to improve the 454 native base-calling error rate, pyrobayes was used to transform the native 454 quality values into the standard phred64 quality scores . following this, transcriptome raw reads were trimmed using clean_reads and snowhite […]


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PyroBayes in publications

 (21)
PMCID: 5344015
PMID: 28286717
DOI: 10.7717/peerj.3071

[…] 3′) as detailed by . pyrosequencing was performed using a roche/454 flx+ instrument and titanium chemistry kits according to the manufacturer’s instructions. sff file processing was done using pyrobayes () and inspected for chimeric sequences using pintail () and error corrected using acacia (). further trimming was done in qiime () with sequence length 300–600 bases, no ambiguous […]

PMCID: 4996412
PMID: 27600241
DOI: 10.3390/microarrays4040570

[…] fluorescence colors., to interpret the sequencing data and to accurately identify the snps of interest, bioinformatics algorithms for searching snps have been developed, including tablet [], pyrobayes [], soap [], varscan [], maq [], magicviewer [], atlas-snp2 []. hence, snp discovery can also result from dna resequencing analysis using novel deep-sequencing strategies. although […]

PMCID: 4148237
PMID: 25167074
DOI: 10.1371/journal.pone.0104739

[…] to amplify the v1 to v3 region of the 16s rrna gene. sequencing was performed on a roche/454 flx+ genome sequencer according to manufacturer’s instructions. the data pre-processing was done using pyrobayes followed by further analysis in qiime v1.6.0 using usearch, uchime and uclust algorithms at sequence similarity threshold of 97% and blast taxonomy assignments. sequences were trimmed […]

PMCID: 3999722
PMID: 24727571
DOI: 10.1093/brain/awu060

[…] (patients 1, 2, 4, 5, 6 and 7) was performed with tagged primers and ultra deep sequencing achieved using a roche 454 gs titanium flx platform as previously described (). an analysis pipeline of pyrobayes, mosiak, and a custom r library was used to call and align the sequences to the mitochondrial dna reference along with a control cloned mitochondrial dna sequence. for quality control […]

PMCID: 3948169
PMID: 24603808
DOI: 10.1371/journal.pone.0090842

[…] gs flx sequencer at nanjing forestry university. all ests in this study were deposited in ncbi with an accession number srr1037160., raw 454 sequence files in sff format were base-called using the pyrobayes base caller . in addition, 78,689 peach ests were downloaded from genbank in february 2012. the 454 sequencing data and genbank ests were processed with gs flx v2.0.01 software (454 life […]


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PyroBayes institution(s)
Department of Biology, Boston College, Chestnut Hill, MA, USA
PyroBayes funding source(s)
Supported by a grant from the US National Human Genome Research Institute (R01 HG003698).

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