Bandage: interactive visualisation ofde novogenome assemblies [PDF]
Bioinformatics, 2015 AbstractSummaryWhilede novoassembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (aBioinformaticsApplication forNavigatingDe novoAssemblyGraphsEasily) is a tool for visualising assembly graphs with connections.
Wick, RR +3 more
openaire +3 more sources
Genomics Data, 2015 Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence.
Kiran Gopinath Bankar +3 more
doaj +1 more source
Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes [PDF]
, 2015 The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next ...
Cuomo, Christina A +11 more
core +2 more sources
Telescoper: de novo assembly of highly repetitive regions. [PDF]
, 2012 MotivationWith advances in sequencing technology, it has become faster and cheaper to obtain short-read data from which to assemble genomes. Although there has been considerable progress in the field of genome assembly, producing high-quality de novo ...
Bresler, Ma'ayan +3 more
core +1 more source
Leveraging multiple sequencing technologies to generate a haplotype specific assembly of sugarcane R570. [W1018] [PDF]
, 2020 While sugarcane is one of the world's most important economic grasses for its sugar production and biofuel potential, tools and resources to understand its genetics are lacking.
Aitken, Karen S. +8 more
core
BIGMAC : breaking inaccurate genomes and merging assembled contigs for long read metagenomic assembly. [PDF]
, 2016 BackgroundThe problem of de-novo assembly for metagenomes using only long reads is gaining attention. We study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement.
Clum, Alicia +3 more
core +2 more sources
A comparative evaluation of genome assembly reconciliation tools
Genome Biology, 2017 Background The majority of eukaryotic genomes are unfinished due to the algorithmic challenges of assembling them. A variety of assembly and scaffolding tools are available, but it is not always obvious which tool or parameters to use for a specific ...
Hind Alhakami +2 more
doaj +1 more source
G3: Genes, Genomes, Genetics, 2020 In recent years, improved sequencing technology and computational tools have made de novo genome assembly more accessible. Many approaches, however, generate either an unphased or only partially resolved representation of a diploid genome, in which ...
llya Soifer +14 more
doaj +1 more source
What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual. [PDF]
, 2015 BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a ...
Alexander, Leeson J +9 more
core +1 more source
dnAQET: a framework to compute a consolidated metric for benchmarking quality of de novo assemblies
BMC Genomics, 2019 Background Accurate de novo genome assembly has become reality with the advancements in sequencing technology. With the ever-increasing number of de novo genome assembly tools, assessing the quality of assemblies has become of great importance in genome ...
Gokhan Yavas, Huixiao Hong, Wenming Xiao
doaj +1 more source