Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on the 10 January 2020, with the hope of turning the table against the worsening pandemic situation. Previous studies in respiratory
virus characterization require mapping of raw sequences to the human genome in the downstream bioinformatics pipeline as part of metagenomic principles. Illumina, as the major player in the NGS arena, took action by releasing guidelines for improved enrichment kits called the Respiratory Virus Oligo Panel (RVOP) based on a hybridization capture method capable of capturing targeted respiratory viruses, including SARS-CoV-2; therefore, allowing a direct map of raw sequences data
to SARS-CoV-2 genome in downstream bioinformatics pipeline. Consequently, two bioinformatics pipelines emerged with no previous studies benchmarking the pipelines. This study focuses on gaining insight and understanding of target enrichment workflow by Illumina through the utilization of different bioinformatics pipelines named as ‘Fast Pipeline’ and ‘Normal Pipeline’ to SARS-CoV-2 strains isolated from Yogyakarta and Central Java, Indonesia. Overall, both pipelines work well in the
characterization of SARS-CoV-2 samples, including in the identification of major studied nucleotide
substitutions and amino acid mutations. A higher number of reads mapped to the SARS-CoV-2
genome in Fast Pipeline and merely were discovered as a contributing factor in a higher number of
coverage depth and identified variations (SNPs, insertion, and deletion). Fast Pipeline ultimately
works well in a situation where time is a critical factor. On the other hand, Normal Pipeline would
require a longer time as it mapped reads to the human genome. Certain limitations were identified in
terms of pipeline algorithm, whereas it is highly recommended in future studies to design a pipeline
in an integrated framework, for instance, by using NextFlow, a workflow framework to combine all
scripts into one fully integrated pipeline.
Rumpun Ilmu
Ilmu Komputer
Bahasa Asli/Original Language
English
Level
Internasional
Status
Dokumen Karya
No
Judul
Tipe Dokumen
Aksi
1
genes-13-01330-v2.pdf
[PAK] Full Dokumen
2
Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains.pdf
