A1 Refereed original research article in a scientific journal

Kuura—An automated workflow for analyzing WES and WGS data




AuthorsJambulingam Dhanaprakash, Rathinakannan Venkat Subramaniam, Heron Samuel, Schleutker Johanna, Fey Vidal

PublisherPublic Library of Science (PLoS)

Publication year2024

JournalPLoS ONE

Journal name in sourcePloS one

Volume19

Issue1

eISSN1932-6203

DOIhttps://doi.org/10.1371/journal.pone.0296785

Web address https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0296785

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/387230360


Abstract

The advent of high-throughput sequencing technologies has revolutionized the field of genomic sciences by cutting down the cost and time associated with standard sequencing methods. This advancement has not only provided the research community with an abundance of data but has also presented the challenge of analyzing it. The paramount challenge in analyzing the copious amount of data is in using the optimal resources in terms of available tools. To address this research gap, we propose "Kuura-An automated workflow for analyzing WES and WGS data", which is optimized for both whole exome and whole genome sequencing data. This workflow is based on the nextflow pipeline scripting language and uses docker to manage and deploy the workflow. The workflow consists of four analysis stages-quality control, mapping to reference genome & quality score recalibration, variant calling & variant recalibration and variant consensus & annotation. An important feature of the DNA-seq workflow is that it uses the combination of multiple variant callers (GATK Haplotypecaller, DeepVariant, VarScan2, Freebayes and Strelka2), generating a list of high-confidence variants in a consensus call file. The workflow is flexible as it integrates the fragmented tools and can be easily extended by adding or updating tools or amending the parameters list. The use of a single parameters file enhances reproducibility of the results. The ease of deployment and usage of the workflow further increases computational reproducibility providing researchers with a standardized tool for the variant calling step in different projects. The source code, instructions for installation and use of the tool are publicly available at our github repository https://github.com/dhanaprakashj/kuura_pipeline.


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Last updated on 2024-26-11 at 13:26