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Downloads and Upgrades: UCSC Genome Browser Group and Opal 1.7


The genome browser group at the University of California, Santa Cruz has released an updated genes track for the human genome browser. The new release has 82,960 total transcripts, compared with 80,922 in the previous version and the total number of canonical genes has increased from 31,227 to 31,848.

The group has also released assembly data hubs, which extend the functionality of track data hubs to assemblies that are not hosted natively on the browser. These hubs were developed to help researchers annotate sequences for which UCSC does not provide an annotation database. They let users include the underlying reference sequence, as well as data tracks that annotate that sequence. Sequences are stored in the UCSC twoBit format, and the annotation tracks are stored in the same manner as track data hubs.

Omicia has released version 1.7 of Opal, its cloud-based genome interpretation software.

Opal offers tools to analyze genomes and prioritize disease-causing variants and genes. These include a pipeline that lets users assess and compare the quality of genome variant files, methods to filter out polymorphic genes, and a reporting tool that lets users share results.

The Scan

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.