GoldRush, Stash and miBF mapper presented at ISMB 2022

The 30th conference on Intelligent Systems for Molecular Biology (ISMB 2022) will be held in a hybrid format (in Madison, Wisconsin, USA and virtually) from July 10-14, 2022. The Bionformatics Technology Lab will be presenting various new algorithms and data structures developed by the group in the past year. We are introducing our new de novo long read assembly tool, GoldRush, a modular and memory-efficient genome assembler with linear time complexity. Presentations by three of our members will describe the major steps and developments in GoldRush. In addition, we are presenting our new data structure based on stochastic tile hashing, Stash, and our new long read mapping tool using the multi-index Bloom filter.

Oral Presentations:

Johnathan Wong at HitSeq COSI: GoldRush-Path: A de novo assembler for long reads with linear time complexity
Armaghan Sarvar at HitSeq COSI: Stash: A data structure based on stochastic tile hashing

Poster Presentations:

Johnathan Wong at HitSeq COSI: GoldRush-Path: A de novo assembler for long reads with linear time complexity
Vladimir Nikolic at HitSeq COSI: GoldRush-Edit : A targeted, alignment-free polishing & finishing pipeline for long read assembly, using long read k-mers
Lauren Coombe at HitSeq COSI: GoldRush-Link: Integrating minimizer-based overlap detection and gap-filling to the ntLink long read scaffolder
Armaghan Sarvar at HitSeq COSI: Stash: A data structure based on stochastic tile hashing
Talha Murathan Goktas at HitSeq COSI: Mapping noisy long-reads with the multi-index Bloom filter: miBF-mapper
Vladimir Nikolic at HitSeq COSI: btllib: A C++ library with Python interface for efficient sequence processing

The participation of Johnathan Wong, Vladimir Nikolic and Lauren Coombe at ISMB 2022 was partially funded by generous contributions from the John Jambor Education Fund. BTL projects presented at ISMB 2022 are supported thanks to funds from Genome BC, Genome Canada and the National Institutes of Health (NIH).