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Protocols

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

Versioning


No version available

Documentation


Maintainers


  • person_outline Aaron Quinlan
  • person_outline Gabor Marth

Publication for PyroBayes

PyroBayes citations

 (26)
library_books

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens

2017
PeerJ
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 […]

library_books

Efficient SNP Discovery by Combining Microarray and Lab on a Chip Data for Animal Breeding and Selection

2015
Microarrays
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 […]

call_split

Comparison of fecal and cecal microbiotas reveals qualitative similarities but quantitative differences

2015
BMC Microbiol
PMCID: 4403768
PMID: 25887695
DOI: 10.1186/s12866-015-0388-6
call_split See protocol

[…] 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 […]

library_books

Differential Responses of Cecal Microbiota to Fishmeal, Eimeria and Clostridium perfringens in a Necrotic Enteritis Challenge Model in Chickens

2014
PLoS One
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 […]

call_split

Resequencing the susceptibility gene, ITGAM, identifies two functionally deleterious rare variants in systemic lupus erythematosus cases

2014
PMCID: 4060450
PMID: 24886912
DOI: 10.1186/ar4566
call_split See protocol

[…] 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; […]

library_books

Mutations in the SPG7 gene cause chronic progressive external ophthalmoplegia through disordered mitochondrial DNA maintenance

2014
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 […]


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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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