Analysis of Coronavirus outbreak data with Pharo 8.x
Metacello new baseline: 'COVID19'; repository: 'github://hernanmd/COVID-2019/src'; load.
For visualization of cases as provided by CSSEGISandData, evaluate in Pharo 8:
For genomic analysis install BioSmalltalk and evaluate the following one-liner to align the sequences with MAFFT:
To add accession numbers as they appear in the NCBI GenBank repository, edit the class side methods matching the sequencing location:
The resulting alignment is written in 'mafft_output.align' in the Pharo image directory.
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.
To create a GitHub Pharo project with Continuous Integration support from scrath follow this video.
- 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.