This is Scott; my contract working on GMOD related tasks (including JBrowse, Chado, and Tribal) and other projects like wormbase.org and alliancegenome.org/ is likely to come to and end soon. If you know of anybody looking for help with things like this, (1/2)
Did you know that you could get variant analysis, methylation and phasing in a single data analysis workflow? #EPI2ME human variation workflow, best practice @nanopore data analysis, with great reports and integrated genome browser. #nanoporeconf
I created a Colab tutorial that checks if a gene/transcript ID has an associated crystal structure, checks if related proteins with associated crystal structures are available, and then compares those to a de novo structure prediction:
colab.research.google.com/gi…
The application even includes jbrowse2 for no fuss viewing of read alignments straight. Analysis a manual review in a single application.
jbrowse.org/jb2/
I am happy to announce that the #JBrowse2 paper has be published in Genome Bio. There is lots of cool stuff: synenty, structural variation, plugins, multi chromosome and multi genome views, a graphical configuration editor, a desktop and easy-to-embed apps genomebiology.biomedcentral.…
ALT Seven panels: A The Linear Genome View displaying gene annotations, quant signals, and a Hi-C track. B whole genome overview showing tumor vs normal sequencing coverage in the COLO829 cell line. C The Circular View gives an overview of long-range relationships within and between chromosomes (translocations in an SKBR3 cancer genome). D The Dotplot View shows relationships between two sequences (in this case the relationship between hg19 and hg38 human genomes). E The Tabular View summarizes features in a sortable, filterable list, showing in this example the SKBR3 variant calls from Sniffles. F The Linear Synteny View shows relationships between two genomes (in this case, peach and grape). G The SV Inspector allows inspection of structural variants by combining a Tabular View and a Circular View. H The Breakpoint Split View shows events such as gene fusions and translocations by aligning two Linear Genome Views and tracing the split or paired read mappings across the two views
It's that time again: I'm going to start bugging people for letters of support for the @usejbrowse project. If you have time and are a #JBrowse user, please consider writing a letter. JBrowse is a big part of many genomics projects, and we want to make sure it continues to grow.
#GMOD at #PAG today: #JBrowse workshop 1:30 in T&C D (including hands on tutorial), #JBrowse from an implementer's perspective in Next Gen Annotation in Pacific E at 4:20 (blaze!)
Darn it, I forgot to include useful things like time and location (I've gotten used to longer posts elsewhere so was worried about keeping it brief!): the session is at 4:00 in Town & Country D (the computer demo room)
JBrowse v2.2.0 released, featuring alignments track performance improvements, totally revamped documentation on our website, and lazy loading of assemblies allowing improved scalability for loading many genomes in a single config! See release notes: jbrowse.org/jb2/blog/2022/11…