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bioviz.bsky.social
BioViz
@bioviz.bsky.social
20 followers 36 following 5 posts
Open source genome visualization for everyone featuring the Integrated Genome Browser, free for all from BioViz.org.
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bioviz.bsky.social
BioViz @bioviz.bsky.social · Jun 27
Deepthi made a cool new App! It's an IGB track filter. It hides alignments of sequence reads that contain really big gaps, an artifact (usually) from running RNA-to-genome alignment algorithms without setting a maximum intron size parameter. apps.bioviz.org/apps/reads-w...
This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left. This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left.
Reposted by BioViz
bar-plantbio.bsky.social
If you want to learn more about single cell approaches for plant biolgy, join us in Portland, Maine August 10-15. The application deadline has been extended to July 21st. We've got a great roster of speakers and topics! www.grc.org/single-cell-...
2025 Single-Cell Approaches in Plant Biology Conference GRC
The 2025 Gordon Research Conference on Single-Cell Approaches in Plant Biology will be held in Portland, Maine. Apply today to reserve your spot.
www.grc.org
July 17, 2025 at 8:11 PM
Reposted by BioViz
seqera.io
Register below! hubs.la/Q03xrdRC0
Professional Services in Life Sciences: Scaling From Proof-of-Concept to Enterprise-Wide Deployment | Seqera
We built Nextflow to empower individuals to run analyses more efficiently. Now, we’re helping the world's leading pharma organizations do the same. When scaling scientific platforms, the journey matt...
hubs.la
July 16, 2025 at 9:56 AM
Reposted by BioViz
sib.swiss
Depuis 25 ans, le SIB développe des bases de données ouvertes comme UniProt/Swiss-Prot grâce à des fonds publics. Elles sont cruciales pour la recherche et l’IA, mais leur pérennité est menacée. @dessimoz.bsky.social en parle dans Le Temps : www.letemps.ch/sciences/c-e...
«C’est une réelle menace pour les progrès de la science»: à la suite des coupes américaines, les chercheurs suisses craignent pour leurs données - Le Temps
Les scientifiques redoutent des entraves dans la collecte et le partage des résultats de recherche à travers le monde, à la suite de l’offensive anti-science de l’administration Trump. Certains appell...
www.letemps.ch
July 2, 2025 at 10:00 AM
bioviz.bsky.social
Nextflow training. training.nextflow.io/latest/hello...
Hello Nextflow - training.nextflow.io
training.nextflow.io
June 28, 2025 at 11:23 PM
bioviz.bsky.social
Deepthi made a cool new App! It's an IGB track filter. It hides alignments of sequence reads that contain really big gaps, an artifact (usually) from running RNA-to-genome alignment algorithms without setting a maximum intron size parameter. apps.bioviz.org/apps/reads-w...
This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left. This screen capture from the IGB App Store shows the page for Deepthi's cool new App called "Monster Alignment Filter." The page explains how to use the app and what it's most useful for. Basically, it lets you hide all the sequence read alignments in a track that are too big for the genome. Normally, we use alignments with gaps to define or predict intron locations in gene models. However, aligners sometimes place aligned sequence blocks far from each other, in places that don't make biological sense. This makes it look like introns in the target genome can be much larger than is reasonable given the species. This App lets you filter out these suspicious alignments and focus on what's left.
June 27, 2025 at 5:35 PM
Reposted by BioViz
lablabella.bsky.social
Looking 👀 at your data, even BIG data, is critical.

Paige Kulzer shows #Evol2025 #Evol25 how the Integrated Genome Browser (IGB) @bioviz.bsky.social can help you discover 🔎 cool genomic patterns

IGB is free, compatible with common file types, and intuitive to use!
June 21, 2025 at 3:19 PM
Reposted by BioViz
drandreahoward.bsky.social
This JUST came up again and @ruben.the100.ci pointed me to the @malte.the100.ci blog explaining how to do it:
June 10, 2025 at 9:26 PM
bioviz.bsky.social
Here's an image showing two tracks of single-cell RNA-Seq data from tomato aligned using STARsolo. One track shows what happens when you don't set the maximum intron parameter. The result: Lots of alignments that are way, way, way too big! Our advice: Always view your alignments in a genome browser.
An image from Integrated Genome Browser showing two tracks. Both tracks contain data from SRA accession SRR30982326 aligned using STARsolo at UseGalaxy.eu. The parameters used for each track were the same, except that the top track specified parameter --alignIntronMax 5000. The vertical zoom is set so that you can see all alignments in the region are visible. There are thousands, and so each individual alignment looks like a thin horizontal line in this view. Hopefully, you can see that when we use the default maximum intron size, many apparently spurious alignments get created that extend far outside the gene shown in the gene models track. However, in the top track, it looks like there may be another gene upstream of the gene that is shown. We've seen this type of thing many times in the past with plant genomes. Plant genomes generally have very small introns (compared to mammals) and often have multiple duplicated genes side-by-side on the same chromosome. This makes alignments -- and assemblies! -- difficult sometimes.
June 11, 2025 at 6:37 PM
bioviz.bsky.social
Welcome to our new social media account! We'll be posting images and news about Integrated Genome Browser and genome visualization here. Please follow to keep up with our latest greatest work.
June 11, 2025 at 6:12 PM