https://zodo.asu.edu/zoophy/

Pipeline for virus phylodynamics via BEAST v.1.10x

Relevant articles:

1. Scotch M, Mei C, Brandt C, Sarkar IN, Cheung K. At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. Epidemiology. 2010 Nov;21(6):764-8.

https://zodo.asu.edu/geoboost2/

Natural language processing tool for enrichment of geographic metadata of virus sequence records

Relevant Articles:

1. Magge A, Weissenbacher D, O'Connor K, Tahsin T, Gonzalez-Hernandez G, Scotch M. GeoBoost2: a natural languageprocessing pipeline for GenBank metadata enrichment for virus phylogeography. Bioinformatics. 2020 Dec 22;36(20):5120-5121.

2. Tahsin T, Weissenbacher D, O'Connor K, Magge A, Scotch M, Gonzalez-Hernandez G. GeoBoost: accelerating research involving the geospatial metadata of virus GenBank records. Tahsin T, Weissenbacher D, O'Connor K, Magge A, Scotch M, Gonzalez-Hernandez G.

https://github.com/ZooPhy/radx

A bioinformatics pipeline for analysis of high-throughput sequencing data of SARS-CoV-2 from wastewater

Relevant Articles:

1. Fontenele RS, Kraberger S, Hadfield J, Driver EM, Bowes D, Holland LA, Faleye TOC, Adhikari S, Kumar R, Inchausti R, Holmes WK, Deitrick S, Brown P, Duty D, Smith T, Bhatnagar A, Yeager RA 2nd, Holm RH, von Reitzenstein NH, Wheeler E, Dixon K, Constantine T, Wilson MA, Lim ES, Jiang X, Halden RU, Scotch M, Varsani A. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res. 2021 Oct 15;205:117710.