Projects with Sergey Koren, PhD

Associate Investigator

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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.

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

MetAMOS

A metagenomic and isolate assembly and analysis pipeline [ retired ]

Celera Assembler PBcR

PacBio read correction and assembly pipeline [ retired ]

Bambus 2

Metagenomic scaffolding and variant detection [ retired ]

AMOS

A modular sequence assembly infrastructure [ retired ]