DOI: 10.5061/dryad.g52m3
title: Data from: RAD sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference

description: Restriction site-associated DNA sequencing (RADseq) provides researchers
 with the ability to record genetic polymorphism across thousands of loci
 for non-model organisms, potentially revolutionising the field of
 molecular ecology. However, as with other genotyping methods, RADseq is
 prone to a number of sources of error that may have consequential effects
 for population genetic inferences, and these have received only limited
 attention in terms of the estimation and reporting of genotyping error
 rates. Here we use individual sample replicates, under the expectation of
 identical genotypes, to quantify genotyping error in the absence of a
 reference genome. We then use sample replicates to (1) optimize de novo
 assembly parameters within the program Stacks, by minimizing error and
 maximizing the retrieval of informative loci, and; (2) quantify error
 rates for loci, alleles and SNPs. As an empirical example we use a double
 digest RAD dataset of a non-model plant species, Berberis alpina,
 collected from high altitude mountains in Mexico.
description: 0.Demultiplexing and
 dropbaseContains the custom Perl
 scripts of the pipeline used to demultiplex raw reads and drop a base
 position that was causing a lane effect.Demultiplexing_and_dropbase.zip1.Running StacksContains 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*1stacks.zip2.R analyses of Stacks outputsContains 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.2R.zipData (SRA SRP035472)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.Sampling localitiesCointains 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. pallidaSampling_localities_Berberis.xlsFiguresContains 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 repositoryLab protocol and sequencing reportContains: 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.LabProtocol_and_sequencing_report.zip