Projects with Sergey Koren, PhD
Associate Investigator
Verkko
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.
GQC (Genome Quality Checker)
GQC is a benchmarking tool for evaluating sequence reads and assemblies against a genome benchmark.
TTT
Trivial Tangle Traverser (TTT) is a tool developed to construct model sequences for the remaining gaps in the T2T assemblies and replace error-prone and labour-intensive manual graph curation step.
Verkko-Fillet
Post-verkko graph and assembly curation in Python
T2T-Polish
Evaluation and polishing workflows for T2T genome assemblies
Merfin
Evaluate variant calls and its combination with k-mer multiplicity
Merqury
Evaluate genome assemblies with k-mers and more
Winnowmap
A long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
MetaMaps
Long-read metagenomic analysis
SALSA
A tool to scaffold long read assemblies with Hi-C data
MashMap
A fast and approximate long read mapper
Canu
A single molecule sequence assembler for genomes large and small
Mash
Fast genome and metagenome distance and containment estimation using MinHash
MHAP
A probabilistic sequence overlap algorithm