دورية أكاديمية

Detailed installation and usage instructions.

التفاصيل البيبلوغرافية
العنوان: Detailed installation and usage instructions.
المؤلفون: Dhanaprakash Jambulingam, Venkat Subramaniam Rathinakannan, Samuel Heron, Johanna Schleutker, Vidal Fey
سنة النشر: 2024
مصطلحات موضوعية: Genetics, Molecular Biology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, throughput sequencing technologies, standard sequencing methods, pipeline scripting language, kuura &# 8212, quality score recalibration, consensus call file, gatk haplotypecaller <, wgs data ”, div >< p, 2 ), generating, variant calling step, variant recalibration, variant consensus, variant calling, varscan <, strelka <, nextflow <, freebayes <, docker <, deepvariant <, whole exome, updating tools, time associated, source code, research gap
الوصف: 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 , VarScan 2, Freebayes and Strelka 2), 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_pipelineTest .
نوع الوثيقة: article in journal/newspaper
اللغة: unknown
العلاقة: https://figshare.com/articles/journal_contribution/Detailed_installation_and_usage_instructions_/25023223Test
DOI: 10.1371/journal.pone.0296785.s001
الإتاحة: https://doi.org/10.1371/journal.pone.0296785.s001Test
https://figshare.com/articles/journal_contribution/Detailed_installation_and_usage_instructions_/25023223Test
حقوق: CC BY 4.0
رقم الانضمام: edsbas.1A339598
قاعدة البيانات: BASE