Towards many colors in FISH on 3D-preserved interphase nuclei [PDF]
, 2006 The article reviews the existing methods of multicolor FISH on nuclear targets, first of all, interphase chromosomes. FISH proper and image acquisition are considered as two related components of a single process.
Albiez, H. +9 more
core +1 more source
Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum [PDF]
Applied and Environmental Microbiology, 2005 ABSTRACT Rhodospirillum rubrum is a phototrophic purple nonsulfur bacterium known for its unique and well-studied nitrogen fixation and carbon monoxide oxidation systems and as a source of hydrogen and biodegradable plastic production.
Reslewic, Susan +13 more
openaire +4 more sources
AGORA: Assembly Guided by Optical Restriction Alignment
BMC Bioinformatics, 2012 Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs).
Lin Henry C +6 more
doaj +1 more source
A clone-free, single molecule map of the domestic cow (Bos taurus) genome. [PDF]
, 2015 BackgroundThe cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals.
Bechner, Michael +11 more
core +1 more source
SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner [PDF]
, 2013 To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of
Chang Yu +16 more
core +6 more sources
The hidden perils of read mapping as a quality assessment tool in genome sequencing [PDF]
, 2017 This article provides a comparative analysis of the various methods of genome sequencing focusing on verification of the assembly quality. The results of a comparative assessment of various de novo assembly tools, as well as sequencing technologies, are ...
A Bankevich +14 more
core +1 more source
Analysis of Brachypodium genomes with genome-wide optical maps
Genome, 2018 Brachypodium distachyon (n = 5) is a diploid and has been widely used as a genetic model. Brachypodium stacei (n = 10) and B. hybridum (n = 15) are species that are related to B. distachyon, leading to an hypothesis that they are part of a polyploid series based on x = 5. Several lines of evidence suggest that this hypothesis is incorrect and that the
Zhu, Tingting +7 more
openaire +3 more sources
nanotatoR: a tool for enhanced annotation of genomic structural variants
BMC Genomics, 2021 Background Whole genome sequencing is effective at identification of small variants, but because it is based on short reads, assessment of structural variants (SVs) is limited. The advent of Optical Genome Mapping (OGM), which utilizes long fluorescently
Surajit Bhattacharya +3 more
doaj +1 more source
Optical mapping of the Fusarium oxysporum f. sp. melongenae genome [PDF]
Journal of Basic Microbiology, 2021 Abstract Optical mapping approaches are widely preferred and applied in different branches of genomic studies because of their accuracy, low cost, and high efficiency. In the current study, a sequence orientation of the Fusarium oxysporum f.
Duygu Ates +2 more
openaire +6 more sources
Are we there yet? : reliably estimating the completeness of plant genome sequences [PDF]
, 2016 Genome sequencing is becoming cheaper and faster thanks to the introduction of next-generation sequencing techniques. Dozens of new plant genome sequences have been released in recent years, ranging from small to gigantic repeat-rich or polyploid genomes.
Ruttink, Tom +2 more
core +3 more sources