A survey of mapping algorithms in the long-reads era
It has been over a decade since the first publication of a method dedicated entirely to
mapping long-reads. The distinctive characteristics of long reads resulted in methods …
mapping long-reads. The distinctive characteristics of long reads resulted in methods …
[HTML][HTML] From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
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 …
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …
Protein-to-genome alignment with miniprot
H Li - Bioinformatics, 2023 - academic.oup.com
Motivation Protein-to-genome alignment is critical to annotating genes in non-model
organisms. While there are a few tools for this purpose, all of them were developed over 10 …
organisms. While there are a few tools for this purpose, all of them were developed over 10 …
GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis
Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …
GenStore: A high-performance in-storage processing system for genome sequence analysis
Read mapping is a fundamental step in many genomics applications. It is used to identify
potential matches and differences between fragments (called reads) of a sequenced …
potential matches and differences between fragments (called reads) of a sequenced …
FPGA-based near-memory acceleration of modern data-intensive applications
Modern data-intensive applications demand high computational capabilities with strict
power constraints. Unfortunately, such applications suffer from a significant waste of both …
power constraints. Unfortunately, such applications suffer from a significant waste of both …
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter
the ongoing pandemic. Predicting lineage abundance from wastewater, however, is …
the ongoing pandemic. Predicting lineage abundance from wastewater, however, is …
Efficient mapping of accurate long reads in minimizer space with mapquik
DNA sequencing data continue to progress toward longer reads with increasingly lower
sequencing error rates. We focus on the critical problem of mapping, or aligning, low …
sequencing error rates. We focus on the critical problem of mapping, or aligning, low …
Accelerating genome analysis: A primer on an ongoing journey
Genome analysis fundamentally starts with a process known as read mapping, where
sequenced fragments of an organism's genome are compared against a reference genome …
sequenced fragments of an organism's genome are compared against a reference genome …
SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence mapping
A critical step of genome sequence analysis is the mapping of sequenced DNA fragments
(ie, reads) collected from an individual to a known linear reference genome sequence (ie …
(ie, reads) collected from an individual to a known linear reference genome sequence (ie …