nucmer

<p>The "nucmer.snps" variant file is obtained by processing the SARS-Cov-2 sequence
from Gisaid website (complete, high coverage only, low coverage exclusion, Host=human,
Virus name = hCoV-19) with "seqkit" software and "nucmer" scripts. The example data
is downsampled from complete data in 2020-07-28 (0.001 proportion, 52 samples).</p>

datasets

A feasible framework for mutation analysis and reverse transcription
polymerase chain reaction (RT-PCR) assay evaluation of COVID-19, including
mutation profile visualization, statistics and mutation ratio of each assay.
The mutation ratio is conducive to evaluating the coverage of RT-PCR assays in
large-sized samples. Mercatelli, D. and Giorgi, F. M. (2020)
<doi:10.20944/preprints202004.0529.v1>.

Shaoqian Ma

CovidMutations

Mutation Analysis Toolkit for COVID-19 (Coronavirus Disease
2019)

Yongyou Zhang

nucmer function

<p>A dataframe with 437 rows (mutation sites) and 14 columns.</p>

State of Data and AI Literacy Report 2025

nucmer: Mutation information derived from "nucmer" SNP analysis

Description

Usage

Arguments

Format

Examples