Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
10231878 | Computational Biology and Chemistry | 2014 | 37 Pages |
Abstract
The success of a short-read based genome assembly process in faithfully reproducing the sequences of a real genome, or its genes, can be modulated by some or all of three key parameters: read length r, insert size I, and a bioinformatics parameter, the word length k (k-mer length), which is used in most modern assembly tools based on de Bruijn graphs. The present study focuses on how plots of simple assembly success metrics, and their variation as a function of k, can serve as succinct graphical representations of how the assembly process deals with a given genomic context.
Related Topics
Physical Sciences and Engineering
Chemical Engineering
Bioengineering
Authors
Juan Esteban Gallo, José Fernando Muñoz, Elizabeth Misas, Juan Guillermo McEwen, Oliver Keatinge Clay,