Metagenomic data assembly–the way of decoding unknown microorganisms

AL Lapidus, AI Korobeynikov - Frontiers in Microbiology, 2021 - frontiersin.org
Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …

Recent advances in assembly of complex plant genomes

W Kong, Y Wang, S Zhang, J Yu… - Genomics, Proteomics & …, 2023 - academic.oup.com
Over the past 20 years, tremendous advances in sequencing technologies and
computational algorithms have spurred plant genomic research into a thriving era with …

Spike2vec: An efficient and scalable embedding approach for covid-19 spike sequences

S Ali, M Patterson - 2021 IEEE international conference on big …, 2021 - ieeexplore.ieee.org
With the rapid global spread of COVID-19, more and more data related to this virus is
becoming available, including genomic sequence data. The total number of genomic …

Computational graph pangenomics: a tutorial on data structures and their applications

JA Baaijens, P Bonizzoni, C Boucher, G Della Vedova… - Natural computing, 2022 - Springer
Computational pangenomics is an emerging research field that is changing the way
computer scientists are facing challenges in biological sequence analysis. In past decades …

A reconfigurable fefet content addressable memory for multi-state hamming distance

L Liu, AF Laguna, R Rajaei, MM Sharifi… - … on Circuits and …, 2023 - ieeexplore.ieee.org
Pattern searches, a key operation in many data analytic applications, often deal with data
represented by multiple states per dimension. However, hash tables, a common software …

Complex genome assembly based on long-read sequencing

T Zhang, J Zhou, W Gao, Y Jia, Y Wei… - Briefings in …, 2022 - academic.oup.com
High-quality genome chromosome-scale sequences provide an important basis for
genomics downstream analysis, especially the construction of haplotype-resolved and …

Enhanced recovery of microbial genes and genomes from a marine water column using long-read metagenomics

JM Haro-Moreno, M López-Pérez… - Frontiers in …, 2021 - frontiersin.org
Third-generation sequencing has penetrated little in metagenomics due to the high error
rate and dependence for assembly on short-read designed bioinformatics. However, second …

StrainXpress: strain aware metagenome assembly from short reads

X Kang, X Luo, A Schönhuth - Nucleic acids research, 2022 - academic.oup.com
Next-generation sequencing–based metagenomics has enabled to identify microorganisms
in characteristic habitats without the need for lengthy cultivation. Importantly, clinically …

Big data analytics capability as a major antecedent of firm innovation performance

A Muhammad, CK Yu, A Qadir… - The International …, 2022 - journals.sagepub.com
Purpose: This study aimed to investigate the big data analytics capabilities (BDAC) model
using resource-based theory (RBT) and dimensions of big data analytics (management …

Accelerating large scale de novo metagenome assembly using GPUs

MG Awan, S Hofmeyr, R Egan, N Ding… - Proceedings of the …, 2021 - dl.acm.org
Metagenomic workflows involve studying uncultured microorganisms directly from the
environment. These environmental samples when processed by modern sequencing …