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PyRAD specifications

Information


Unique identifier OMICS_03724
Name PyRAD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Deren A. R. Eaton

Publication for PyRAD

PyRAD citations

 (38)
library_books

An optimized approach for local de novo assembly of overlapping paired end RAD reads from multiple individuals

2018
R Soc Open Sci
PMCID: 5830760
PMID: 29515871
DOI: 10.1098/rsos.171589

[…] the second reads for assembly, and therefore the information for the first reads was lost. There are several software for the assembly of RAD data supporting PE reads, such as Stacks [,], Rainbow [], pyRAD [] and dDocent []. However, many of these tools cannot directly and fully support RPE datasets with staggered PE reads. There are many studies which did not make full use of RPE reads either for […]

library_books

Genome wide SNP data and morphology support the distinction of two new species of Kovarikia Soleglad, Fet and Graham, 2014 endemic to California (Scorpiones, Vaejovidae)

2018
Zookeys
PMCID: 5904437
PMID: 29674883
DOI: 10.3897/zookeys.739.20628

[…] g Laboratory at UC Berkeley for 150-base single-end sequencing on one lane of an Illumina HiSeq4000 (combined with 10 pooled libraries in the lane).We demultiplexed and processed Illumina reads using pyRAD v2.16.1 (, ). Sequences were clustered at 90% similarity within samples using USEARCH v7.0.1090 () and aligned with MUSCLE v3.8.31 (). Error rate and heterozygosity were jointly estimated from t […]

library_books

RADpainter and fineRADstructure: Population Inference from RADseq Data

2018
Mol Biol Evol
PMCID: 5913677
PMID: 29474601
DOI: 10.1093/molbev/msy023

[…] core Stacks populations program. A third party utility script (https://github.com/edgardomortiz/fineRADstructure-tools; last accessed February 24, 2018) also enables conversion from the format of the pyRAD and ipyrad toolkits (). Finally, our input format is a simple flat text file and we provide an example data set to enable the users of other pipelines to prepare their data. […]

library_books

Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes

2018
PMCID: 5829208
PMID: 29445022
DOI: 10.1098/rspb.2017.2732

[…] The conservative concatenated dataset generated by pyRAD consisted of 44 521 bases of sequence which contained 7879 variable sites, 5591 of which were parsimony informative, with 5.9% missing data across all taxa. Both the Bayesian and maximum likelih […]

library_books

Genome wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories

2018
PLoS One
PMCID: 5783331
PMID: 29364919
DOI: 10.1371/journal.pone.0190555

[…] t the genotypes and the read depth per site for every individual sample in the dataset. Given that one of the main aims of this study is the species delimitation of B. tabaci cryptic complex, we used PyRAD, an additional pipeline developed specifically for RADseq data looking at introgression and phylogenetic inferences. The advantage of this pipeline is that it takes into account the insertions a […]

call_split

Integrating restriction site associated DNA sequencing (RAD seq) with morphological cladistic analysis clarifies evolutionary relationships among major species groups of bee orchids

2018
Ann Bot
PMCID: 5786241
PMID: 29325077
DOI: 10.1093/aob/mcx129
call_split See protocol

[…] ttings. Only a subset of the pairs could be overlapped through this approach. We then employed the resulting contigs of variable length (i.e. between 96 and 180 bp) to build a catalogue of loci using pyRAD v.3.0.63 (). This software package allows for indels (expected in the phylogenetic framework of our study) and for unequal length of input sequences (resulting from overlapping read pairs) when […]

Citations

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PyRAD institution(s)
Committee on Evolutionary Biology, University of Chicago, IL, USA; Botany Department, Field Museum of Natural History, IL, USA
PyRAD funding source(s)
This research was supported by a National Science Foundation Dissertation Improvement Grant (DEB-1110598).

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