Results 11 to 20 of about 334,258 (285)
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 +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 +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 +14 more
doaj +1 more source
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 ) an extension strategy that uses whole
Te-Chin, Chu +5 more
openaire +2 more sources
Improving ancient DNA genome assembly [PDF]
PeerJ, 2017 Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used.
Alexander Seitz, Kay Nieselt
doaj +2 more sources
ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data
BMC Bioinformatics, 2021 Background Metagenomics is the study of microbial genomes for pathogen detection and discovery in human clinical, animal, and environmental samples via Next-Generation Sequencing (NGS). Metagenome de novo sequence assembly is a crucial analytical step in
Zachary Deng, Eric Delwart
doaj +1 more source
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. [PDF]
PLoS ONE, 2016 Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies.
Loren A Honaas +9 more
doaj +1 more source
Exploiting sparseness in de novo genome assembly [PDF]
BMC Bioinformatics, 2012 The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments. In this paper, we demonstrate that constructing a sparse assembly graph which stores only a small fraction of the observed k- mers as nodes and the links between these nodes allows the de novo ...
Ye, Chengxi +4 more
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Accurate long-read de novo assembly evaluation with Inspector
Genome Biology, 2021 Long-read de novo genome assembly continues to advance rapidly. However, there is a lack of effective tools to accurately evaluate the assembly results, especially for structural errors.
Yu Chen +4 more
doaj +1 more source
EPGA2: memory-efficient de novo assembler [PDF]
Bioinformatics, 2015 Abstract Motivation: In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.
Junwei, Luo +6 more
openaire +2 more sources