setu: a bioinformatics pipeline to assemble CoViD genome
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel human-infecting strain of Betacoronavirus. This pathogen responsible for the ongoing CoronaVirusDisease (CoViD2019) pandemic. Rapid advancement and declining costs of high throughput sequencing technologies have allowed the virus to be sequenced globally in many individuals affected. While next generation sequencing (NGS) technology offers a robust means of identifying possible pathogens from clinical specimens, easy and user-friendly bioinformatics pipelines are required to achieve a full viral genome sequence and with utmost accuracy.Towards this effort, we have written a detailed pipeline for analyzing and decoding SARS-CoV 2 sequencing data utilizing open source utilities. It involves comprehensive sequence subtraction of host- or bacteria-related NGS reads before de novo assembly, resulting in the rapid and correct assembly of metagenomic sequences of viral genomes
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