Results 31 to 40 of about 99,235 (279)

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology [PDF]

, 2016
Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different
Aguiar, Edgar L., Azevedo, Vasco A. C., Barh, Debmalya, Benevides, Leandro, Figueiredo, Henrique C. P., Folador, Edson L., Ghosh, Preetam, Guimarães, Luís C., Mariano, Diego C. B., Oliveira, Letícia C., Pereira, Felipe L., Ramos, Rommel T. J., Silva, Artur, Sousa, Thiago J.   +13 more
core   +3 more sources

Optical mapping approaches to molecular genomics

Current Opinion in Biotechnology, 1997
A variety of physical mapping methods exist for the analysis of nucleic acids or genomes, including hybridization, sequence tagged site mapping, restriction enzyme fingerprinting, radiation hybrid mapping and optical mapping. Single-molecule approaches offer numerous advantages, including very high resolution, small sample size requirements, and ...
D C, Schwartz, A, Samad
openaire   +2 more sources

Optical mapping as a routine tool for bacterial genome sequence finishing

BMC Genomics, 2007
Background In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts.
Gaudriault Sophie, Forst Steve, Du Zijin, Darby Creg, Bode Helge B, Barbazuk Brad, Miller Nancy, Henkhaus John, Goldman Barry S, Norton Stacie, Latreille Phil, Goodner Brad, Goodrich-Blair Heidi, Slater Steven   +13 more
doaj   +1 more source

Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions

Plants, 2023
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors.
Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne   +10 more
doaj   +1 more source

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., Benecletti, P. A., Bolzer, A., Cremer, M., Cremer, T., Joffe, B., Müller, Stefan, Solovei, Irina, Speicher, Michael R., Walter, J.   +9 more
core   +1 more source

OMSim : a simulator for optical map data [PDF]

, 2017
Motivation: The Bionano Genomics platform allows for the optical detection of short sequence patterns in very long DNA molecules (up to 2.5 Mbp). Molecules with overlapping patterns can be assembled to generate a consensus optical map of the entire ...
Audenaert, Pieter, Fostier, Jan, Miclotte, Giles, Plaisance, Stéphane, Rombauts, Stephane, Van de Peer, Yves   +5 more
core   +2 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, Goldstein Steve, Mendelowitz Lee, Zhou Shiguo, Wetzel Joshua, Schwartz David C, Pop Mihai   +6 more
doaj   +1 more source

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, Vandepoele, Klaas, Veeckman, Elisabeth   +2 more
core   +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, Hayk Barseghyan, Emmanuèle C. Délot, Eric Vilain   +3 more
doaj   +1 more source

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, AV Karlyshev, D Antipov, EW Myers, HC Lin, IJ Tsai, J Parkhill, K Rutherford, M Hunt, M Land, MT Swain, S Lin, S Meader, TD Otto, TJ Carver   +14 more
core   +1 more source