Sam Kovaka

Computational biology postdoc at JHU

[Sam Kovaka @samkovaka]

@JonathanGoeke @mike_schatz @timp0 That is available at https://t.co/OyUM84sNNE. Just updated the README with the link, thank you for the reminder!

[Michael Schatz @mike_schatz]

Very excited to announce "Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment" by @samkovaka et al. https://t.co/nnn3CMLWkr

[Nature Methods @naturemethods]

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
https://t.co/GteZYRggcL

[Sam Kovaka @samkovaka]

@Hasindu2008 @lachlanjmc @Psy_Fer_ A similar plot can be generated with Uncalled4's "dotplot" (https://t.co/JukaFe7HQn). 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!

[Sam Kovaka @samkovaka]

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

[Sam Kovaka @samkovaka]

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: https://t.co/q6WwHepg1K

[Michael Schatz @mike_schatz]

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. https://t.co/GfzF2khXM2

[Sam Kovaka @samkovaka]

@mike_schatz @JohnsHopkins @JHUCompSci @HopkinsBio @JHU_BDPs Congratulations!!

[bioRxiv Bioinfo @biorxiv_bioinfo]

Pan-genomic Matching Statistics for Targeted Nanopore Sequencing https://t.co/ct4mdiOLYS #biorxiv_bioinfo

[Nature Reviews Genetics @NatureRevGenet]

DNA SEQUENCING: Complex targeted sequencing in real time https://t.co/IasiElRA4M #ResearchHighlight

[Michael Schatz @mike_schatz]

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. https://t.co/dtZxL48XQo

[Sam Kovaka @samkovaka]

@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

[Sam Kovaka @samkovaka]

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! https://t.co/8xGRYEVkmX

[Sam Kovaka @samkovaka]

@mike_schatz @miranext @sbarnettARK The AGBT talk wasn't recorded, but here is a short talk I gave for BCC2020: https://t.co/cwNUh2ZSAu

[Sam Kovaka @samkovaka]

@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.

[Sam Kovaka @samkovaka]

@mattloose We are, thanks! I've temporarily moved to a different state and just being safe. Hope you're doing (relatively) well too.

[Sam Kovaka @samkovaka]

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 https://t.co/nsN33IyUkr

[Sam Kovaka @samkovaka]

@sbarnettARK @mike_schatz I should be there for most of the 1:30-3pm poster session today!

[bioRxiv @biorxivpreprint]

Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED https://t.co/HHyJ8YThGe #bioRxiv

[Genome Biology @GenomeBiology]

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 https://t.co/gnMbVyAWEY