Scientific abstracts describing long sequencing read genome assembler GoldRush and data structure Stash, accepted for oral presentations at ISMB 2022conference ·
The 30th conference on Intelligent Systems for Molecular Biology (ISMB 2022) is taking place in Madison, WI (USA) July 10-14, 2022 and the BTL group will attend in person to showcase our work on de novo long read genome assembler with linear time complexity, GoldRush, and its key components (golden path algorithm GoldRush-Path, long read scaffolder GoldRush-Link and long read polisher GoldRush-Edit). We will also present btllib, a C++ code library with Python interface we built for efficient sequence processing and introduce a new data structure for describing nucleotide sequences with lossy representation, Stash (based on stochastic tile hashing), which can be used to efficiently store and query sequence mapping information. Stay tuned for presentation URLs.
Johnathan Wong at HiTSeq COSI. “GoldRush-Path: A de novo assembler for long reads with linear time complexity”
Lauren Coombe at HiTSeq COSI. “GoldRush-Link: Integrating minimizer-based overlap detection and gap-filling into the ntLink long read scaffolder”
Vladimir Nikolic at HiTSeq COSI. “GoldRush-Edit : A targeted, alignment-free polishing & finishing pipeline for long read assembly, using long read k-mers”
and “btllib: A C++ library with Python interface for efficient sequence processing”
Armaghan Sarvar at HiTSeq COSI. “Stash: A data structure based on stochastic tile hashing”
BTL projects to be presented at ISMB 2022 are supported thanks to funds from Genome BC, Genome Canada and the National Institutes of Health.