Projects with Sergey Koren, PhD
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.
Evaluate genome assemblies with k-mers and more
A long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
Long-read metagenomic analysis
A tool to scaffold long read assemblies with Hi-C data
A fast and approximate long read mapper
A single molecule sequence assembler for genomes large and small
Fast genome and metagenome distance and containment estimation using MinHash
A probabilistic sequence overlap algorithm
A metagenomic and isolate assembly and analysis pipeline [ retired ]
Celera Assembler PBcR
PacBio read correction and assembly pipeline [ retired ]
Metagenomic scaffolding and variant detection [ retired ]
A modular sequence assembly infrastructure [ retired ]