RT Journal Article
SR Electronic
T1 Figbird: A probabilistic method for filling gaps in genome assemblies
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.11.24.469861
DO 10.1101/2021.11.24.469861
A1 Sumit Tarafder
A1 Mazharul Islam
A1 Swakkhar Shatabda
A1 Atif Rahman
YR 2021
UL http://biorxiv.org/content/early/2021/11/25/2021.11.24.469861.abstract
AB Motivation Advances in sequencing technologies have led to sequencing of genomes of a multitude of organisms. However, draft genomes of many of these organisms contain a large number of gaps due to repeats in genomes, low sequencing coverage and limitations in sequencing technologies. Although there exist several tools for filling gaps, many of these do not utilize all information relevant to gap filling.Results Here, we present a probabilistic method for filling gaps in draft genome assemblies using second generation reads based on a generative model for sequencing that takes into account information on insert sizes and sequencing errors. Our method is based on the expectation-maximization (EM) algorithm unlike the graph based methods adopted in the literature. Experiments on real biological datasets show that this novel approach can fill up large portions of gaps with small number of errors and misassemblies compared to other state of the art gap filling tools.Availability and Implementation The method is implemented using C++ in a software named “Filling Gaps by Iterative Read Distribution (Figbird)”, which is available at: https://github.com/SumitTarafder/Figbird.Contact atif{at}cse.buet.ac.bdSupplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.