Abstract
Evolutionary biology has entered an era of unprecedented amounts of DNA sequence data, as new sequencing technologies such as Massive Parallel Sequencing (MPS) can generate billions of nucleotides within less than a day. The current bottleneck is how to efficiently handle, process, and analyze such large amounts of data in an automated and reproducible way. To tackle these challenges we introduce the Sequence Capture Processor (SECAPR) pipeline for processing raw sequencing data into multiple sequence alignments for downstream phylogenetic and phylogeographic analyses. SECAPR is user-friendly and we provide an exhaustive empirical data tutorial intended for users with no prior experience with analyzing MPS output. SECAPR is particularly useful for the processing of sequence capture (synonyms: target or hybrid enrichment) datasets for non-model organisms, as we demonstrate using an empirical sequence capture dataset of the palm genus Geonoma (Arecaceae). Various quality control and plotting functions help the user to decide on the most suitable settings for even challenging datasets. SECAPR is an easy-to-use, free, and versatile pipeline, aimed to enable efficient and reproducible processing of MPS data for many samples in parallel.
Highlights
An increasing number of studies apply sequence data generated by Massive Parallel Sequencing (MPS) to answer phylogeographic and phylogenetic questions (e.g., BoteroCastro et al, 2013; Smith et al, 2014a; Smith et al, 2014b; Faircloth et al, 2015; Heyduk et al, 2016)
Phylogenetic analysis software usually relies on multiple sequence alignments (MSAs) with homologous sequences across many taxa, which are simple to recover when enriching these sequences prior to sequencing
Here we introduce the Sequence Capture Processor (SECAPR) pipeline, a semi-automated workflow to guide users from raw sequencing results to cleaned and filtered multiple sequence alignments (MSAs) for phylogenetic and phylogeographic analyses
Summary
An increasing number of studies apply sequence data generated by Massive Parallel Sequencing (MPS) to answer phylogeographic and phylogenetic questions (e.g., BoteroCastro et al, 2013; Smith et al, 2014a; Smith et al, 2014b; Faircloth et al, 2015; Heyduk et al, 2016). Researchers often decide to selectively enrich and sequence specific genomic regions of interest, rather than sequencing the complete genome. One reason is that enriching specific markers leads to a higher sequencing depth for each individual marker, as compared to the alternative of sequencing full genomes. How to cite this article Andermann et al (2018), SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments. Phylogenetic analysis software usually relies on multiple sequence alignments (MSAs) with homologous sequences across many taxa, which are simple to recover when enriching these sequences prior to sequencing
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