Mikhail Kolmogorov
@mishakolmogorov.bsky.social
Tenure-track Stadtman Investigator at NIH/NCI. I like computational/cancer/metagenomics. The views are my own.
With our collaborators, we sequenced 6 tumor/normal cell lines with ONT, HiFi and Illumina with the goal to provide comprehensive somatic variant benchmarks. We benchmarked tools against a consensus SV set and Severus did pretty good:
October 24, 2023 at 4:57 PM
With our collaborators, we sequenced 6 tumor/normal cell lines with ONT, HiFi and Illumina with the goal to provide comprehensive somatic variant benchmarks. We benchmarked tools against a consensus SV set and Severus did pretty good:
A bit on methods: Severus built on the breakpoint graph framework, a popular way to model genome rearrangements. In cancer, we often have "catastrophic" SVs that fracture and rearrange chromosome segments.
October 24, 2023 at 4:57 PM
A bit on methods: Severus built on the breakpoint graph framework, a popular way to model genome rearrangements. In cancer, we often have "catastrophic" SVs that fracture and rearrange chromosome segments.
Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...
October 24, 2023 at 4:56 PM
Today we announce the first release of Severus: a new tool for somatic SV calling for long reads! It's designed for complex (and simple) rearrangements in cancer genomes, but also works well for germline github.com/KolmogorovLa...
I'll be talking about metagenome assemblies at Microbiome Data Congress 2023 (November 13-14 in Boston). Looks like it's going to be fun! Registration: microbiome-data.com/register
October 19, 2023 at 3:37 PM
I'll be talking about metagenome assemblies at Microbiome Data Congress 2023 (November 13-14 in Boston). Looks like it's going to be fun! Registration: microbiome-data.com/register
Most importantly, our WDL pipeline is not called Napu (Nanopore analysis pipeline 4 U), which is this adorable critter below! Feel free to give it a try and let us know if you have any feedback: github.com/nanoporegeno...
September 14, 2023 at 6:35 PM
Most importantly, our WDL pipeline is not called Napu (Nanopore analysis pipeline 4 U), which is this adorable critter below! Feel free to give it a try and let us know if you have any feedback: github.com/nanoporegeno...