Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis

05/16/2022
by   Mohammed Alser, et al.
0

We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major computational bottlenecks and inefficiencies throughout the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are still not able to read a genome in its entirety. We describe the ongoing journey in significantly improving the performance, accuracy, and efficiency of genome analysis using intelligent algorithms and hardware architectures. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches for each step of the genome analysis pipeline and provide experimental evaluations. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory) along with algorithmic changes, leading to new hardware/software co-designed systems. We conclude with a foreshadowing of future challenges, benefits, and research directions triggered by the development of both very low cost yet highly error prone new sequencing technologies and specialized hardware chips for genomics. We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent. The analysis script and data used in our experimental evaluation are available at: https://github.com/CMU-SAFARI/Molecules2Variations

READ FULL TEXT

page 3

page 8

page 12

research
07/30/2020

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Genome analysis fundamentally starts with a process known as read mappin...
research
02/21/2022

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis

Read mapping is a fundamental, yet computationally-expensive step in man...
research
09/18/2022

GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping

Nanopore sequencing is a widely-used high-throughput genome sequencing t...
research
04/01/2020

Computational Performance of a Germline Variant Calling Pipeline for Next Generation Sequencing

With the booming of next generation sequencing technology and its implem...
research
04/30/2023

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

High-throughput sequencing (HTS) technologies have revolutionized the fi...
research
01/03/2021

Segmentation and genome annotation algorithms

Segmentation and genome annotation (SAGA) algorithms are widely used to ...
research
04/18/2018

Bayesian Metabolic Flux Analysis reveals intracellular flux couplings

Metabolic flux balance analyses are a standard tool in analysing metabol...

Please sign up or login with your details

Forgot password? Click here to reset