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Assembling genomes from single-cell sequencing data is essential for single-cell studies. However, single-cell assemblies are challenging due to (i) the highly non-uniform read coverage and (ii) the elevated levels of sequencing errors and chimeric reads. In this study, we present a new framework called EPGA-SC for de novo assembly of single-cell sequencing reads. The EPGA assembler has designed strategies to solve the problems caused by sequencing errors, sequencing biases and repetitive regions. However, the extremely unbalanced and richer error types prevent EPGA to achieve high performance in single-cell sequencing data. In this study, we designed EPGA-SC based on EPGA. The main innovations of EPGA-SC are as follows: (i) classifying reads to reduce the proportion of false reads; (ii) using multiple sets of high precision paired-end reads generated from the high precision assemblies produced by other assembler such as SPAdes to overcome the impact of sequencing biases and repetitive regions; (iii) developing novel algorithms for removing chimeric errors and extending contigs. We test EPGA-SC with seven datasets. The experimental results show that EPGA-SC can generate better assemblies than most current tools in most time in term of MAX contig, N50, NG50, NA50 and NGA50.
This article was published in the following journal.
Name: IEEE/ACM transactions on computational biology and bioinformatics
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Major constituent of the cytoskeleton found in the cytoplasm of eukaryotic cells. They form a flexible framework for the cell, provide attachment points for organelles and formed bodies, and make communication between parts of the cell possible.
Techniques of nucleotide sequence analysis that increase the range, complexity, sensitivity, and accuracy of results by greatly increasing the scale of operations and thus the number of nucleotides, and the number of copies of each nucleotide sequenced. The sequencing may be done by analysis of the synthesis or ligation products, hybridization to preexisting sequences, etc.
A genotoxicological technique for measuring DNA damage in an individual cell using single-cell gel electrophoresis. Cell DNA fragments assume a "comet with tail" formation on electrophoresis and are detected with an image analysis system. Alkaline assay conditions facilitate sensitive detection of single-strand damage.
The residual framework structure of the CELL NUCLEUS that maintains many of the overall architectural features of the cell nucleus including the nuclear lamina with NUCLEAR PORE complex structures, residual CELL NUCLEOLI and an extensive fibrogranular structure in the nuclear interior. (Advan. Enzyme Regul. 2002; 42:39-52)
Surface ligands that mediate cell-to-cell adhesion and function in the assembly and interconnection of the vertebrate nervous system. These molecules promote cell adhesion via a homophilic mechanism. These are not to be confused with NEURAL CELL ADHESION MOLECULES, now known to be expressed in a variety of tissues and cell types in addition to nervous tissue.
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