SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

PeerJ
Tobias AndermannAlexandre Antonelli

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 paral...Continue Reading

References

Mar 3, 2009·Genome Research·Jared T SimpsonInanç Birol
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
Mar 27, 2012·Briefings in Bioinformatics·Iain MilneDavid Marshall
Mar 4, 2014·Genome Biology·Martin HuntThomas D Otto
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Sep 12, 2014·Nature·Brian Tilston SmithRobb T Brumfield
May 23, 2015·Molecular Cell·Jason A ReuterMichael P Snyder
May 18, 2018·Systematic Biology·Tobias AndermannAlexandre Antonelli

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Citations

Mar 11, 2020·Frontiers in Genetics·Tobias AndermannAlexandre Antonelli
Aug 17, 2020·Systematic Biology·Daniel M Portik, John J Wiens
Aug 3, 2021·Applications in Plant Sciences·Lars NauheimerKatharina Nargar
Jun 20, 2021·Systematic Biology·Wenbin ZhouQiu-Yun Jenny Xiang
Aug 3, 2021·Applications in Plant Sciences·Todd G B McLayChris J Jackson
Nov 12, 2021·Molecular Phylogenetics and Evolution·Kevin P MulderGuillermo Velo-Antón
Nov 21, 2021·Molecular Ecology Resources·Max R Bangs, Scott J Steppan

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Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

SAMtools
GATK
LASTZ
PHYLUCE
Trimmomatic
Trinity
BLASTZ
Abyss
Geonoma
SECAPR

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