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Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Efficient Synergistic De Novo Co-Assembly Of Bacterial Genomes From Single Cells Using Colored De Bruijn Graph, Narjes Sadat Movahedi Tabrizi
Wayne State University Dissertations
Recent progress in DNA amplification techniques, particularly multiple displacement
amplification (MDA), has made it possible to sequence and assemble bacterial
genomes from a single cell. However, the quality of single cell genome assembly has
not yet reached the quality of normal multi-cell genome assembly due to the coverage
bias (including uneven depth of coverage and region blackout) and errors caused by
MDA. Computational methods try to mitigates the amplification bias. In this document
we introduce a de novo co-assembly method using colored de Bruijn graph,
which can overcome the problem of blackout regions due to amplification bias. The
algorithm is …
De Novo Co-Assembly Of Bacterial Genomes From Multiple Single Cells, Narjes Sadat Movahedi Tabrizi
De Novo Co-Assembly Of Bacterial Genomes From Multiple Single Cells, Narjes Sadat Movahedi Tabrizi
Wayne State University Theses
Recent progress in DNA amplication techniques, particularly multiple displacement amplication (MDA), has made it possible to sequence and assemble bacterial genomes from a single cell. However, the quality of single cell genome assembly has not yet reached the quality of normal multicell genome assembly due to the coverage bias and errors caused by MDA. Using a template of more than one cell for MDA or combining separate MDA products has been shown to improve the result of genome assembly from few single cells, but providing identical single cells, as a necessary step for these approaches, is a challenge. As a …