Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Piñero D, Emerson BC

Date Published: June 10, 2014

DOI: http://dx.doi.org/10.5061/dryad.g52m3

 

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Title 0.Demultiplexing and dropbase
Description Contains the custom Perl scripts of the pipeline used to demultiplex raw reads and drop a base position that was causing a lane effect.
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Title 1.Running Stacks
Description Contains scripts and part of the output data of running *Stacks* with the demultiplexed-lane-effect-corrected data (see section **Demultiplexing and dropbase/0.1DropBase** of this repository) available at the Sequence Read Archive (SRA), accession SRP035472; to subsequently produce SNP (*.SNP) and coverage (*.COV) tsv matrices and to run the *populations* program of Stacks with the selected loci of the downstream analyses. The Stacks parameter values corresponds to the experiments defined as *1) Exploratory analysis of Stacks assembly key parameters and SNP calling model using replicates* and *2) Effect of using different parameters on the output information content and on the detection of genetic structuring*
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Title 2.R analyses of Stacks outputs
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Description Contains the R scripts, input-output data and metainformation used to perform the analyses described in the *General processing of Stacks outputs* and *Error rates* of the manuscript.
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Title Data (SRA SRP035472)
Description The postdemultiplexing quality filtered data (i.e. output of "Demultiplexing and dropbase" of this repository) is available at the Sequence Read Archive (SRA), accession SRP035472. Those files were used to run Stacks and the resulted matrices coverage and SNP matrices produced after running the Stacks script *export_sql.pl* along with the subsequent files used to perform the analyses on R. See contents of the [2R](./2R) directory. For the rest of the pipeline the scripts used and when available and output summary are presented inside each directory.
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Title Sampling localities
Description Cointains and the geographic information of sampling sites. See tab "B.alpina B.moranensis" for Berberis alpina and B. moranensis populations and "Berberis outgroups" for B. trifolia and B. pallida
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Title Figures
Description Contains the R markdown files that were used to generate the Figures from the main text (Figures.Rmd) and the figures from the supporting information (SupportingInfomation_*). Needs the data and scripts from the *2.R analyses of Stacks outputs* section of this repository
Download README.txt (273 bytes)
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Title Lab protocol and sequencing report
Downloaded 1 time
Description Contains: i) a summary of the ddRAD labwork, description of final libraries and sequencing output, ii) modified ddRAD sequencing protocol and iii) sequencing quality control reports for each lane.
Download LabProtocol_and_sequencing_report.zip (2.019 Mb)
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When using this data, please cite the original publication:

Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Piñero D, Emerson BC (2015) RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Molecular Ecology Resources 15(1): 28-41. http://dx.doi.org/10.1111/1755-0998.12291

Additionally, please cite the Dryad data package:

Mastretta-Yanes A, Arrigo N, Alvarez N, Jorgensen TH, Piñero D, Emerson BC (2014) Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g52m3
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