@JonathanGoeke @mike_schatz @timp0 That is available at github.com/skovaka/uncall…. Just updated the README with the link, thank you for the reminder!
English
Sam Kovaka
20 posts
Sam Kovaka
@samkovaka
Computational biology postdoc at JHU
Katılım Ağustos 2011
133 Takip Edilen242 Takipçiler
@mike_schatz @samkovaka @timp0 "This should be used with an m6Anet model trained on Uncalled4 alignments (link coming soon)" looking forward to that!
English
Sam Kovaka retweetledi
Very excited to announce "Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment" by @samkovaka et al. biorxiv.org/content/10.110…
English
Sam Kovaka retweetledi
Bioinformatics advancements unleash the full potential of long-read sequencing in various areas of genomics. A Comment from Michael Schatz (@mike_schatz) and colleagues highlights this thriving domain of active methods development. @JohnsHopkins
nature.com/articles/s4159…
English
@Hasindu2008 @lachlanjmc @Psy_Fer_ A similar plot can be generated with Uncalled4's "dotplot" (github.com/skovaka/UNCALL…). We currently only support signal-to-reference alignment, but I'll look into basecalled alignments in the future. We're still in a pre-release stage, but I'm happy for feedback from early users!
English
@lachlanjmc figure is from an embarrassingly dirty script that I wrote to use bash, slow5tools, f5c, and samtools and matlab. The script is here, but it is a dog's breakfast.
github.com/hasindu2008/si…
perhaps @Psy_Fer_ could make this into squigglekit or @samkovaka to uncalled4 as a feature?
English
f5c resquiggle aligns @nanpore raw-signals to basecalled-reads. Default output is an intuitive, yet bulky TSV. Specifying -c will output a compact PAF-like format with the alignment encoded in a custom CIGAR-like format. Details are documented here hasindu2008.github.io/f5c/docs/output.
Hasindu Gamaarachchi@Hasindu2008
f5c-v1.1 is released and features a new module called resquiggle that aligns raw-signals to basecalled reads [contributed by @hiruna72]. github.com/hasindu2008/f5…
English
Thank you! So happy to finally (pretty much) be a doctor. Also excited to announce that I'll be staying at Hopkins as a postdoc with @mike_schatz!
Michael Schatz@mike_schatz
Congratulations to @samkovaka for defending his thesis on Computational Methods for Genomic, Transcriptomic, and Epi-Omic Analysis with Long-Read Sequencing! @timp0, @elapertea and I are so proud! @nanopore @PacBio @JHUCompSci @HopkinsEngineer
English
Come to my talk on December 2nd! Despite being in the adaptive sampling session, I'll be talking more about general analysis and visualization of nanopore signal. If you think that's uncalled for, well...
Oxford Nanopore Events@NanoporeConf
At #nanoporeconf, @Samkovaka will present UNCALLED4: an adaptive sampling toolkit for nanopore signal alignment & analysis. UNCALLED4 features interactive alignment visualisations & comparisons, & epigenetic modification detection stats: bit.ly/3Gy20sX
English
Sam Kovaka retweetledi
Need lots and lots of reads from your @nanopore for copy number analysis of cancer genomes? Try short molecule sequencing! Impactful project with @TimourBaslan @samkovaka @sedlazeck @shgoodwin1 et al. academic.oup.com/nar/advance-ar…
English
English
Very proud to announce that I was promoted to become the Bloomberg Distinguished Professor of Computer Science and Biology at @JohnsHopkins. So incredibly grateful to my dream team lab, collaborators, friends & family that have supported me @JHUCompSci @HopkinsBio @JHU_BDPs
English
Sam Kovaka retweetledi
Pan-genomic Matching Statistics for Targeted Nanopore Sequencing biorxiv.org/cgi/content/sh… #biorxiv_bioinfo
English
Sam Kovaka retweetledi
DNA SEQUENCING: Complex targeted sequencing in real time go.nature.com/3rSXVbe #ResearchHighlight
English
Sam Kovaka retweetledi
A very simple yet very effective approach: High resolution copy number inference in cancer using short-molecule @nanopore sequencing. Great work with @TimourBaslan @samkovaka @sedlazeck @shgoodwin1 et al. biorxiv.org/content/10.110…
Clarksburg, MD 🇺🇸 English
@aaronquinlan @shfo @mike_schatz @acarroll_ATG The limiting factor for ONT is pore lifetimes, and ReadUntil lets pores spend less time sequencing unwanted reads. It doesn't substantially affect the ratio of on-target/off-target reads, just their lengths. Also, ejected DNA is partially unwound, so unlikely it would rebind
English
@shfo @mike_schatz @acarroll_ATG @samkovaka Yes, but the kicked molecule has the "guide" enzyme still attached, whereas other potential molecules may not. Seems a "wash", but I am obviously missing the critical bit as usual. Time to read the manuscript in detail!
English
This is software which watches the signal of DNA through a single pore, decides it doesn't want that piece of DNA, and gives a command to alter that particular pore. Applied simultaneously to a large array of pores. When you stop to think about it, it's petty mind boggling.
Michael Schatz@mike_schatz
Excited to announce: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Awesome work with @samkovaka, Yunfan Fan, @bohan_ni & @timp0 that will forever change how sequencing is done. @JHUCompSci @JHUBME @nanopore nature.com/articles/s4158…
English
Want to find out about how a class project turned into an @NatureBiotech paper? Read this "Behind the Paper" blog post I wrote about the UNCALLED paper! bioengineeringcommunity.nature.com/posts/software…
English
@mike_schatz @miranext @sbarnettARK The AGBT talk wasn't recorded, but here is a short talk I gave for BCC2020: vimeo.com/437696496
English
English
Awesome to see this #nanopore method for targeted sequencing (UNCALLED) be published! Congrats @samkovaka @mike_schatz and team, and (belated) thanks for the explainer back at AGBT in Feb—where I first heard about UNCALLED.
Michael Schatz@mike_schatz
Excited to announce: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Awesome work with @samkovaka, Yunfan Fan, @bohan_ni & @timp0 that will forever change how sequencing is done. @JHUCompSci @JHUBME @nanopore nature.com/articles/s4158…
English
@liu3zhen @mike_schatz @bohan_ni @timp0 @JHUCompSci @JHUBME @nanopore Thanks! We're working on adding support for direct RNA reads, and depleting ribosomal RNA will be one of the first things we try. In the paper we predict you could enrich the exome by ~3 fold in a simulation, but we haven't been able to try a real run yet due to covid limits.
English
@mike_schatz @samkovaka @bohan_ni @timp0 @JHUCompSci @JHUBME @nanopore Great progress. Congrats! Can we perform mRNA sequencing without removing ribosomal RNA? Can exome-seq be replaced by this strategy?
English
Excited to announce: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Awesome work with @samkovaka, Yunfan Fan, @bohan_ni & @timp0 that will forever change how sequencing is done. @JHUCompSci @JHUBME @nanopore nature.com/articles/s4158…
English
@mattloose We are, thanks! I've temporarily moved to a different state and just being safe. Hope you're doing (relatively) well too.
English
A nice way to end two weeks of quarantine!
Michael Schatz@mike_schatz
Excited to announce: Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Awesome work with @samkovaka, Yunfan Fan, @bohan_ni & @timp0 that will forever change how sequencing is done. @JHUCompSci @JHUBME @nanopore nature.com/articles/s4158…
English
@sbarnettARK @mike_schatz I should be there for most of the 1:30-3pm poster session today!
English
@mike_schatz @samkovaka Any specific window you’ll be there today?
English
Want to hear more about enrichment of Nanopore sequencing with UNCALLED? Come talk to @samkovaka at poster 1007 #agbt20 biorxiv.org/content/10.110…
English
Sam Kovaka retweetledi
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED biorxiv.org/cgi/content/sh… #bioRxiv
English
Sam Kovaka retweetledi
StringTie2 from @samkovaka, @elapertea and co. An update of the popular reference-guided transcriptome assembler, now includes the ability to assemble long reads. It's more accurate than other assemblers, while being quicker with lower memory requirements genomebiology.biomedcentral.com/articles/10.11…
English