title: AMPLISAS: a web server for multilocus genotyping using next-generation amplicon sequencing data.
abstract: Next-generation sequencing (NGS) technologies are revolutionizing the fields of biology and medicine as powerful tools for amplicon sequencing (AS). Using combinations of primers and barcodes, it is possible to sequence targeted genomic regions with deep coverage for hundreds, even thousands, of individuals in a single experiment. This is extremely valuable for the genotyping of gene families in which locus-specific primers are often difficult to design, such as the major histocompatibility complex (MHC). The utility of AS is, however, limited by the high intrinsic sequencing error rates of NGS technologies and other sources of error such as polymerase amplification or chimera formation. Correcting these errors requires extensive bioinformatic post-processing of NGS data. Amplicon Sequence Assignment (AMPLISAS) is a tool that performs analysis of AS results in a simple and efficient way, while offering customization options for advanced users. AMPLISAS is designed as a three-step pipeline consisting of (i) read demultiplexing, (ii) unique sequence clustering and (iii) erroneous sequence filtering. Allele sequences and frequencies are retrieved in excel spreadsheet format, making them easy to interpret. AMPLISAS performance has been successfully benchmarked against previously published genotyped MHC data sets obtained with various NGS technologies.
authors.affiliation: Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
authors.forename: Alvaro
authors.initials: A
authors.lastname: Sebastian
authors.affiliation: Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Herdegen
authors.affiliation: Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
authors.forename: Magdalena
authors.initials: M
authors.lastname: Migalska
authors.affiliation: Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614, Poznan, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Radwan
mesh_terms: D019295:Computational Biology / Q000379:methods*; D060005:Genotyping Techniques; D059014:High-Throughput Nucleotide Sequencing; D020407:Internet; D058885:Multilocus Sequence Typing / Q000379:methods*
keywords: amplicon sequencing; genotyping; major histocompatibility complex; next generation sequencing; web server