hernanmd / COVID-2019

Analysis of Coronavirus outbreak data with Pharo

Introduction

Analysis of Coronavirus outbreak data with Pharo 8.x

Installation

Metacello new
   baseline: 'COVID19';
   repository: 'github://hernanmd/COVID-2019/src';
   load.

Usage

Data Visualization

For visualization of cases as provided by CSSEGISandData, evaluate in Pharo 8:

BioCOVID19Viz exampleLiveData

Alignment

For genomic analysis install BioSmalltalk and evaluate the following one-liner to align the sequences with MAFFT:

BioCOVID19GenomicAnalysis alignSeqs.

To add accession numbers as they appear in the NCBI GenBank repository, edit the class side methods matching the sequencing location:

• seqsFromChina
• seqsFromItaly
• seqsFromUSA
• ...

The resulting alignment is written in 'mafft_output.align' in the Pharo image directory.

Accessions are retrieved from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Wuhan%20seafood%20market%20pneumonia%20virus,%20taxid:2697049

Reference Genome download

To download the latest build of the reference genome (as of 01/02/2020) from NCBI:

BionCoV2019GD new download.

Downloaded files are located into the Pharo image directory.

Misc

To create a GitHub Pharo project with Continuous Integration support from scrath follow this video.

ToDo

• Download accessions from here: https://dev.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml (currently restricted access?)
• Add sequences from GISAID
• Evaluate MAFFT alignment quality.

Sample output