12 papers · ranked by Valyu relevance
Alejandro Hernandez Wences, Michael C. Schatz
Genome assembly projects typically run multiple algorithms in an attempt to find the single best assembly, although those assemblies often have complementary, if untapped, strengths and weaknesses. We present our metassembler algorithm that merges multiple assemblies of a genome into a single superior sequence. We…
Mohammed Sahli, Tetsuo Shibuya
Background Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating…
Song Gao, Denis Bertrand, Niranjan Nagarajan
The assembly of large, repeat-rich eukaryotic genomes continues to represent a significant challenge in genomics. While long-read technologies have made the high-quality assembly of small, microbial genomes increasingly feasible, data generation can be prohibitively expensive for larger genomes. Fundamental advances in…
Juanjo Bermúdez
Genome assembly is a fundamental tool for biological research. Particularly, in microbiology, where budgets per sample are often scarce, it can make the difference between an inconclusive result and a fully valid conclusion. Identifying new strains or estimating the relative abundance of quasi-species in a sample are…
Chengxi Ye, Zhanshan Sam Ma, Charles H Cannon, Mihai Pop + 1 more
'Douglas W Yu'] Background The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. Methods In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed…
Jing-Kai Fang, Yue-Feng Lin, Jun-Han Huang, Yibo Chen + 9 more
Computational biology holds immense promise as a domain that can leverage quantum advantages due to its involvement in a wide range of challenging computational tasks. Researchers have recently explored the applications of quantum computing in genome assembly implementation. However, the issue of repetitive sequences…
Zeinab Taghavi
Background Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue is that deep sequencing of every cell should not be necessary to…
Abhishek Sharma, Dániel Czégel, Michael Lachmann, Christopher P. Kempes + 2 more
'Christopher P. Kempes' 'Sara I. Walker' 'Leroy Cronin'] Scientists have grappled with reconciling biological evolution1,2 with the immutable laws of the Universe defined by physics. These laws underpin life’s origin, evolution and the development of human culture and technology, yet they do not predict the emergence…
Tyler G. Moore, Max H. Garzon, Russell J. Deaton, Ming Dao
Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some…
Felipe A. Louza, Guilherme P. Telles, Steve Hoffmann, Cristina D. A. Ciferri
'Cristina D. A. Ciferri'] Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of the input collection or the data…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
Max Doblas, Oscar Lostes-Cazorla, Quim Aguado-Puig, Cristian Iñiguez + 2 more
Pairwise sequence alignment is a core component of multiple sequencing-data analysis tools. Recent advancements in sequencing technologies have enabled the generation of longer sequences at a much lower price. Thus, long-read sequencing technologies have become increasingly popular in sequencing-based studies. However…