scholarly journals Evaluation of genome scaffolding tools using pooled clone sequencing

2018 ◽  
Vol 42 (6) ◽  
pp. 471-476
Author(s):  
Elif DAL ◽  
Can ALKAN
Keyword(s):  
Clone Sequencing ◽  
Genome Scaffolding

Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing

2009 ◽  
Vol 2 (4) ◽  
pp. 160-167 ◽  
Author(s):  
Patrick M. Gillevet ◽  
Masoumeh Sikaroodi ◽  
Albert P. Torzilli
Keyword(s):  
Salt Marsh ◽  
Fungal Diversity ◽  
Clone Sequencing

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 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 Theories and Applications for Sequencing Randomly Selected Clones

2001 ◽  
Vol 11 (2) ◽  
pp. 274-280
Author(s):  
Michael C. Wendl ◽  
Marco A. Marra ◽  
LaDeana W. Hillier ◽  
Asif T. Chinwalla ◽  
Richard K. Wilson ◽  
...  
Keyword(s):  
Human Chromosome ◽  
The Other ◽  
Chromosome 2 ◽  
Contig Assembly ◽  
Secondary Importance ◽  
Clone Size ◽  
Bac Clones ◽  
Clone Sequencing ◽  
Order Of Magnitude ◽  
Random Approach

Theory is developed for the process of sequencing randomly selected large-insert clones. Genome size, library depth, clone size, and clone distribution are considered relevant properties and perfect overlap detection for contig assembly is assumed. Genome-specific and nonrandom effects are neglected. Order of magnitude analysis indicates library depth is of secondary importance compared to the other variables, especially as clone size diminishes. In such cases, the well-known Poisson coverage law is a good approximation. Parameters derived from these models are used to examine performance for the specific case of sequencing random human BAC clones. We compare coverage and redundancy rates for libraries possessing uniform and nonuniform clone distributions. Results are measured against data from map-based human-chromosome-2 sequencing. We conclude that the map-based approach outperforms random clone sequencing, except early in a project. However, simultaneous use of both strategies can be beneficial if a performance-based estimate for halting random clone sequencing is made. Results further show that the random approach yields maximum effectiveness using nonbiased rather than biased libraries.

scholarly journals Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert

2004 ◽  
Vol 70 (2) ◽  
pp. 973-983 ◽  
Author(s):  
Chris M. Yeager ◽  
Jennifer L. Kornosky ◽  
David C. Housman ◽  
Edmund E. Grote ◽  
Jayne Belnap ◽  
...  
Keyword(s):  
Community Structure ◽  
Chihuahuan Desert ◽  
Nitrogenase Activity ◽  
Colorado Plateau ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Soil Crusts ◽  
Clone Sequencing ◽  
Microcoleus Vaginatus ◽  
Diazotrophic Community

ABSTRACT The objective of this study was to characterize the community structure and activity of N2-fixing microorganisms in mature and poorly developed biological soil crusts from both the Colorado Plateau and Chihuahuan Desert. Nitrogenase activity was approximately 10 and 2.5 times higher in mature crusts than in poorly developed crusts at the Colorado Plateau site and Chihuahuan Desert site, respectively. Analysis of nifH sequences by clone sequencing and the terminal restriction fragment length polymorphism technique indicated that the crust diazotrophic community was 80 to 90% heterocystous cyanobacteria most closely related to Nostoc spp. and that the composition of N2-fixing species did not vary significantly between the poorly developed and mature crusts at either site. In contrast, the abundance of nifH sequences was approximately 7.5 times greater (per microgram of total DNA) in mature crusts than in poorly developed crusts at a given site as measured by quantitative PCR. 16S rRNA gene clone sequencing and microscopic analysis of the cyanobacterial community within both crust types demonstrated a transition from a Microcoleus vaginatus-dominated, poorly developed crust to mature crusts harboring a greater percentage of Nostoc and Scytonema spp. We hypothesize that ecological factors, such as soil instability and water stress, may constrain the growth of N2-fixing microorganisms at our study sites and that the transition to a mature, nitrogen-producing crust initially requires bioengineering of the surface microenvironment by Microcoleus vaginatus.

Assignment of the Acute Phase Response Factor (APRF) Gene to 17q21 by Microdissection Clone Sequencing and Fluorescencein SituHybridization of a P1 Clone

Genomics ◽  
1996 ◽  
Vol 37 (2) ◽  
pp. 264-265 ◽  
Author(s):  
Julie Y. Choi ◽  
Wan Liang Li ◽  
Richard E. Kouri ◽  
Jingwei Yu ◽  
Fa Ten Kao ◽  
...  
Keyword(s):  
Acute Phase ◽  
Acute Phase Response ◽  
Phase Response ◽  
Response Factor ◽  
Clone Sequencing

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

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