#jbrowse2 — Public Fediverse posts

On Day 2 of European Galaxy Days, Anthony Bretaudeau presented 'Modern genome browsing in Galaxy with Jbrowse2'.
Read more: https://usegalaxy.eu/root?tool_id=jbrowse2

@abretaud @galaxyfreiburg
#genomics #jbrowse2 #EGD2025 #genome #galaxyproject #eosc #fair #genome_browsing #open_science

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn I was thinking about the comparison of 2 similar assemblies and came up with a potentially useful visualization. As a test set I used the C. elegans N2 assembly (original) and the VC2010 assembly (a resequencing of the same strain, so it should be very similar). I already compared these 2 with #minimap2 and have that data on #WormBase's #JBrowse2. I wrote a simple script that would take a sorted paf file (minimap2) and find gaps. This is the result: https://wormbase.org/tools/genome/jbrowse2/?session=share-SSR4hA6gzo&password=TFpjE

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

@thebiologistisn oh, well, I’m not an expert on comparative genomics, but I do like #minimap2, mostly because it’s easy, fast and gives reasonable looking results for C. elegans and friends. And, not surprisingly, makes nice looking pictures in #JBrowse2 When I get back to my laptop, I’ll post some pictures (still don’t do much genome browsing on my phone :-)

#JBrowse2 has been a long time coming - seven years in development, ten if you count the first rumblings from Rob Buels. The payoff is an amazingly versatile, fast, and beautiful suite of programs for visualizing general genome annotations, relationships between genomes, and genomic evidence: https://rdcu.be/c98wf

#JBrowse #GenomeBrowser #Genomics #Bioinformatics #GenomeAnnotation #Genome #Genomes