scholarly journals OMGS: Optical Map-Based Genome Scaffolding

2020 ◽  
Vol 27 (4) ◽  
pp. 519-533 ◽  
Author(s):  
Weihua Pan ◽  
Tao Jiang ◽  
Stefano Lonardi
Keyword(s):  
Genome Scaffolding ◽  
Optical Map

scholarly journals OMGS: Optical Map-based Genome Scaffolding

2019 ◽  
Author(s):  
Weihua Pan ◽  
Tao Jiang ◽  
Stefano Lonardi
Keyword(s):  
Genome Assembly ◽  
Large Scale ◽  
De Novo ◽  
Optimization Problems ◽  
Sequence Assembly ◽  
Genome Scaffolding ◽  
Contig Sequence ◽  
Optical Map ◽  
Linkage Information ◽  
Optical Maps

AbstractDue to the current limitations of sequencing technologies,de novogenome assembly is typically carried out in two stages, namely contig (sequence) assembly and scaffolding. While scaffolding is computationally easier than sequence assembly, the scaffolding problem can be challenging due to the high repetitive content of eukaryotic genomes, possible mis-joins in assembled contigs and inaccuracies in the linkage information. Genome scaffolding tools either use paired-end/mate-pair/linked/Hi-C reads or genome-wide maps (optical, physical or genetic) as linkage information. Optical maps (in particular Bionano Genomics maps) have been extensively used in many recent large-scale genome assembly projects (e.g., goat, apple, barley, maize, quinoa, sea bass, among others). However, the most commonly used scaffolding tools have a serious limitation: they can only deal with one optical map at a time, forcing users to alternate or iterate over multiple maps. In this paper, we introduce a novel scaffolding algorithm called OMGS that for the first time can take advantages of multiple optical maps. OMGS solves several optimization problems to generate scaffolds with optimal contiguity and correctness. Extensive experimental results demonstrate that our tool outperforms existing methods when multiple optical maps are available, and produces comparable scaffolds using a single optical map. OMGS can be obtained fromhttps://github.com/ucrbioinfo/OMGS

scholarly journals OMSim: a simulator for optical map data

2017 ◽  
Vol 33 (17) ◽  
pp. 2740-2742 ◽  
Author(s):  
Giles Miclotte ◽  
Stéphane Plaisance ◽  
Stephane Rombauts ◽  
Yves Van de Peer ◽  
Pieter Audenaert ◽  
...  
Keyword(s):  
Optical Map ◽  
Map Data

scholarly journals Genomer — A Swiss Army Knife for Genome Scaffolding

PLoS ONE ◽  
2013 ◽  
Vol 8 (6) ◽  
pp. e66922 ◽  
Author(s):  
Michael D. Barton ◽  
Hazel A. Barton
Keyword(s):  
Genome Scaffolding

scholarly journals Genome scaffolding with PE-contaminated mate-pair libraries

2015 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Rayan Chikhi ◽  
Lars Arvestad
Keyword(s):  
Source Code ◽  
Linear Programs ◽  
Read Pair ◽  
Insert Size ◽  
Essential Step ◽  
Genome Scaffolding ◽  
Mate Pair ◽  
A Genome ◽  
The Impact ◽  
Adapter Sequence

Scaffolding is often an essential step in a genome assembly process,in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed in previous work on integrated scaffolders in end-to-end assemblers such as Allpaths-LG and MaSuRCA but the methods relies on the fact that the orientation is observable, \emph{e.g.}, by finding the junction adapter sequence in the reads. This is not always the case, making orientation and insert size of a read pair stochastic. Furthermore, work on modeling PE-contamination has so far been disregarded in stand-alone scaffolders and the effect that PE-contamination has on scaffolding quality has not been examined before. We have addressed PE-contamination in an update of our scaffolder BESST. We formulate the problem as an Integer Linear Program (ILP) and use characteristics of the problem, such as contig lengths and insert size, to efficiently solve the ILP using a linear amount (with respect to the number of contigs) of Linear Programs. Our results show significant improvement over both integrated and standalone scaffolders. The impact of modeling PE-contamination is quantified by comparison with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in increased number of misassemblies, more conservative scaffolding, and inflated assembly sizes. The model is implemented in BESST. Source code and usage instructions are found at https://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.

scholarly journals Kohdista: an efficient method to index and query possible Rmap alignments

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Martin D. Muggli ◽  
Simon J. Puglisi ◽  
Christina Boucher
Keyword(s):  
Single Molecule ◽  
Restriction Enzymes ◽  
Consensus Approach ◽  
E Coli ◽  
Genome Wide ◽  
Alignment Problem ◽  
Optical Map ◽  
Optical Maps ◽  
Map Data ◽  
Genomic Regions

Abstract Background Genome-wide optical maps are ordered high-resolution restriction maps that give the position of occurrence of restriction cut sites corresponding to one or more restriction enzymes. These genome-wide optical maps are assembled using an overlap-layout-consensus approach using raw optical map data, which are referred to as Rmaps. Due to the high error-rate of Rmap data, finding the overlap between Rmaps remains challenging. Results We present Kohdista, which is an index-based algorithm for finding pairwise alignments between single molecule maps (Rmaps). The novelty of our approach is the formulation of the alignment problem as automaton path matching, and the application of modern index-based data structures. In particular, we combine the use of the Generalized Compressed Suffix Array (GCSA) index with the wavelet tree in order to build Kohdista. We validate Kohdista on simulated E. coli data, showing the approach successfully finds alignments between Rmaps simulated from overlapping genomic regions. Conclusion we demonstrate Kohdista is the only method that is capable of finding a significant number of high quality pairwise Rmap alignments for large eukaryote organisms in reasonable time.

Optical map transformations

1974 ◽  
Vol 10 (2) ◽  
pp. 164-168 ◽  
Author(s):  
Olof Bryngdahl
Keyword(s):  
Optical Map ◽  
Map Transformations

scholarly journals Experimental methods for simultaneous measurement of action potentials and electrograms in isolated heart

2010 ◽  
pp. S71-S80
Author(s):  
J Kolářová ◽  
K Fialová ◽  
O Janoušek ◽  
M Nováková ◽  
I Provazník
Keyword(s):  
Isolated Heart ◽  
Fluorescence Emission ◽  
Motion Artifact ◽  
Heart Tissue ◽  
Monophasic Action Potential ◽  
Fluorescence Measurement ◽  
Advantages And Disadvantages ◽  
Additional Noise ◽  
Potential Map ◽  
Optical Map

Monophasic action potential (MAP) can be recorded from the heart surface by optical method based on fluorescence measurement. The motion of isolated heart during experiment caused additional noise in recorded signal. The motion artifact can be eliminated by ratiometric fluorescence emission measurements. This study is based on experiments in which optical MAP measurement is done by single-wavelength and dualwavelength measurement of fluorescence emission. Both recording setups are presented and their advantages and disadvantages are discussed. MAPs recorded by both methods from isolated rabbit hearts perfused according to Langendorff are presented. Simultaneous electrograms (EG) and MAPs recording are analyzed and measurement of velocity of impulse conduction through heart tissue is presented.

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