Seqdev: an algorithm for constructing genetic elements using comparative assembly
Tasnim Rahman,Hasnain Heickal,Shamira Tabrejee,Miraj Kobad Chowdhury,Sheikh Muhammad Sarwar,Mohammad Shoyaib +5 more
TL;DR: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772.
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Abstract: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for Plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772. The Journal's website is at: http://www.banglajol.info/index.php/PTCB/article/view/29772
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References
Short read fragment assembly of bacterial genomes
Mark Chaisson,Pavel A. Pevzner +1 more
TL;DR: A new Eulerian assembler is presented that generates nearly optimal short read assemblies of bacterial genomes and an approach to assemble reads in the case of the popular hybrid protocol when short and long Sanger-based reads are combined.
SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
TL;DR: The SHARCGS algorithm is a suitable tool for fully exploiting novel sequencing technologies by assembling sequence contigs de novo with high confidence and by outperforming existing assembly algorithms in terms of speed and accuracy.
Extending assembly of short DNA sequences to handle error
William R. Jeck,Josephine A. Reinhardt,David A. Baltrus,Matthew T. Hickenbotham,Vincent Magrini,Elaine R. Mardis,Jeffery L. Dangl,Corbin D. Jones +7 more
TL;DR: This work presents VCAKE (Verified Consensus Assembly by K-mer Extension), a modification of simple k-mer extension that overcomes error by using high depth coverage and shows significant improvements in assembly results on simulated and experimental datasets that include error.
Toward Simplifying and Accurately Formulating Fragment Assembly
TL;DR: The fragment assembly problem is reformulated as one of finding a maximum-likelihood reconstruction with respect to the two-sided Kolmogorov-Smirnov statistic, and it is argued that this is a better formulation of the problem.
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Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals
TL;DR: The ability of deep sequencing of the ITS locus to detect and quantify low-abundant Symbiodinium types, as well as finer-scale diversity below the type level, will enable more robust quantification of local genetic diversity in Symbiod inium populations.