Results 1 to 10 of about 152,624 (261)

Graph Theoretical Strategies in De Novo Assembly [PDF]

IEEE Access, 2022
De novo genome assemblers assume the reference genome is unavailable, incomplete, highly fragmented, or significantly altered as in cancer tissues. Algorithms for de novo assembly have been developed to deal with and assemble a large number of short ...
Nafiseh Jafarzadeh
exaly   +4 more sources

DOGMA: de novo assembly of densely labelled optical DNA maps using a matrix profile approach. [PDF]

PLoS One
In optical genome mapping (OGM), large numbers of individual DNA maps-sequence-specific data series along single DNA molecules-are produced. Such individual maps have to be stitched together in a process called de novo OGM assembly in order to create ...
Dvirnas A, Leal-Garza LM, Abbaspour Z, Fröbrant E, Frykholm K, Wrande M, Sandegren L, Westerlund F, Ambjörnsson T.   +8 more
europepmc   +2 more sources

Comprehensive Analysis of the Influence of Technical and Biological Variations on De Novo Assembly of RNA-Seq Datasets. [PDF]

Bioinform Biol Insights
De novo assembly of transcriptomes from species without reference genome remains a common problem in functional genomics. While methods and algorithms for transcriptome assembly are continually being developed and published, the quality of de novo ...
Sergio Alberto G, Maximo R, Andres R, Sergio L, Norma P.   +4 more
europepmc   +2 more sources

De novo genome assemblies of butterflies [PDF]

GigaScience, 2021
Abstract Background The availability of thousands of genomes has enabled new advancements in biology. However, many genomes have not been investigated for their quality. Here we examine quality trends in a taxonomically diverse and well-known group, butterflies (Papilionoidea), and provide draft, de ...
Emily A Ellis, Caroline G Storer, Akito Y Kawahara   +2 more
openaire   +2 more sources

Empirical evaluation of methods for de novo genome assembly [PDF]

PeerJ Computer Science, 2021
Technologies for next-generation sequencing (NGS) have stimulated an exponential rise in high-throughput sequencing projects and resulted in the development of new read-assembly algorithms.
Firaol Dida, Gangman Yi
doaj   +2 more sources

Assembler for de novo assembly of large genomes [PDF]

Proceedings of the National Academy of Sciences, 2013
Significance Assembling a large genome faces three challenges: assembly quality, computer memory requirement, and execution time. Our developed assembler, JR-Assembler, uses ( a ) a strategy that selects good seeds for contig construction, ( b
Te-Chin, Chu, Chen-Hua, Lu, Tsunglin, Liu, Greg C, Lee, Wen-Hsiung, Li, Arthur Chun-Chieh, Shih   +5 more
openaire   +2 more sources

Competition between Heterochromatic Loci Allows the Abundance of the Silencing Protein, Sir4, to Regulate de novo Assembly of Heterochromatin. [PDF]

PLoS Genetics, 2015
Changes in the locations and boundaries of heterochromatin are critical during development, and de novo assembly of silent chromatin in budding yeast is a well-studied model for how new sites of heterochromatin assemble.
Michelle L Larin, Katherine Harding, Elizabeth C Williams, Noel Lianga, Carole Doré, Sophie Pilon, Éric Langis, Corey Yanofsky, Adam D Rudner   +8 more
doaj   +1 more source

transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation

BMC Bioinformatics, 2023
Background RNA-seq followed by de novo transcriptome assembly has been a transformative technique in biological research of non-model organisms, but the computational processing of RNA-seq data entails many different software tools.
Timothy R. Fallon, Tereza Čalounová, Martin Mokrejš, Jing-Ke Weng, Tomáš Pluskal   +4 more
doaj   +1 more source

Efficient assembly of nanopore reads via highly accurate and intact error correction

Nature Communications, 2021
Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore ...
Ying Chen, Fan Nie, Shang-Qian Xie, Ying-Feng Zheng, Qi Dai, Thomas Bray, Yao-Xin Wang, Jian-Feng Xing, Zhi-Jian Huang, De-Peng Wang, Li-Juan He, Feng Luo, Jian-Xin Wang, Yi-Zhi Liu, Chuan-Le Xiao   +14 more
doaj   +1 more source

Extreme Scale De Novo Metagenome Assembly [PDF]

SC18: International Conference for High Performance Computing, Networking, Storage and Analysis, 2018
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art tools require big shared memory machines and cannot handle contemporary metagenome datasets that exceed Terabytes in ...
Georganas, Evangelos, Egan, Rob, Hofmeyr, Steven, Goltsman, Eugene, Arndt, Bill, Tritt, Andrew, Buluc, Aydin, Oliker, Leonid, Yelick, Katherine   +8 more
openaire   +8 more sources