VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

Abstract

Fast and affordable benchtop sequencers are becoming more important in improving personalized medical treatment. Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge. Here we present VARIFI, a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)). We optimized parameters in VARIFI by analyzing more than 170 amplicon-sequenced cancer samples produced on the Personal Genome Machine (PGM). In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to each identified variant. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g., incorrectly identified homopolymer-associated indels with Ion Torrent). VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction. VARIFI requires little computational experience and no in-house compute power since the analyses are conducted on our server. VARIFI is a web-based tool available at varifi.cibiv.univie.ac.at.

Analysis of Basidiomycete Fungal Communities in Soil and Wood from Contrasting Zones of the AWPA Biodeterioration Hazard Map across the United States

“…Taxonomy was assigned using a combination of UTAX and global alignment (USEARCH [28]) to the UNITE database [29] and non-fungal OTUs were removed prior to downstream data processing. OTUs were used for this study, but the authors do acknowledge the growing preference for the use of amplicon sequence variants (ASVs) as they provide greater taxonomic resolution [30][31][32], but for the purpose of this study, OTUs were the preferred output based on our sampling and downstream data analysis methods.…”