Related papers: Aligning sequence reads, clone sequences and assem…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…
Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory architectures alleviate this bottleneck by providing the memory with computing…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…