VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

Abstract

Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation. It supports multiple NGS platforms and has four methodological choices for variant detection. Further, it can re-analyze existing data with alternate thresholds and generates easily interpretable reports in html and tab-delimited formats. Using VDAP-GUI, we have analyzed a publically available human whole-exome sequence dataset. VDAP-GUI is developed using Perl/Tk programming, and is available for free download and use at http://sourceforge.net/projects/vdapgui/.Electronic supplementary materialThe online version of this article (doi:10.1007/s13205-016-0382-1) contains supplementary material, which is available to authorized users.

De novo Assembly and Genome-Wide SNP Discovery in Rohu Carp, Labeo rohita

“…We sampled 3 individuals from each population and pooled their DNA for paired-end Illumina sequencing. The VDAP-GUI pipeline (Menon et al, 2016) was used for genome wide SNP discovery. Commonly used linux command (head-number of reads "filename.fastq" > "filename.fastq") was used to extract the number of reads equivalent to the sample having lowest number of reads and then the data were pooled together to make one dataset for mapping against draft genome.…”

Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping

“…However, standalone pipelines are mostly applied in the high-performance computing environments (HPC). In this study, we have selected and evaluated eleven different WGS and WES pipelines of all three different types, which includes DNAp (Causey et al, 2018), STORMseq (Karczewski et al, 2014), ExScaliburn (Bao et al, 2015), Atlas2 (Evani et al, 2012), MC-GenomeKey (Elshazly et al, 2016), Simplex (Fischer et al, 2012), Whole Exome sequencing Pipeline web tool (WEP) (D'Antonio et al, 2013), SeqBench (Dander et al, 2014), VDAP-GUI (Menon et al, 2016), and fastq2vcf (Gao, Xu & Starmer, 2015).…”

“…VDAP-GUI is a fully automated standalone pipeline, designed for non-IT scientists (Menon et al, 2016). It can analyze WES and WGS data produced by Illumina, Roche 454, and Ion torrent platforms.…”

Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics

“…Once a contig is rendered, it can be used as a proxy to a reference genome. Genome annotation (Nagasaki et al, 2013; Menon et al, 2016), on the other hand, is direct analysis of the reads by two steps. In the first step, each read is annotated using tools such as BLAST (Altschul et al, 1990), functional annotations using tools such as InterProScan (Jones et al, 2014), or pathways by sequence similarities to known enzymes.…”