@inproceedings{3fc79679730c465684208ef865b825a8,
title = "Estimating viral haplotypes in a population using k-mer counting",
abstract = "Viral haplotype estimation in a population is an important problem in virology. Viruses undergo a high number of mutations and recombinations during replication for their survival in host cells and exist as a population of closely related genetic variants. Due to this, estimating the number of haplotypes and their relative frequencies in the population becomes a challenging task. The usage of a sequenced reference genome has its limitations due to the high mutational rates in viruses. We propose a method for estimating viral haplotypes based only on the counts of k-mers present in the viral population without using the reference genome. We compute k-mer pairs that are related to each other by one mutation, and compute a minimal set of viral haplotypes that explain the whole population based on these k-mer pairs. We compare our method to the software ShoRAH (which uses a reference genome) on simulated dataset and obtained comparable results, even without using a reference genome.",
author = "Raunaq Malhotra and Shruthi Prabhakara and Mary Poss and Raj Acharya",
year = "2013",
doi = "10.1007/978-3-642-39159-0_24",
language = "English (US)",
isbn = "9783642391583",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "265--276",
booktitle = "Pattern Recognition in Bioinformatics - 8th IAPR International Conference, PRIB 2013, Proceedings",
address = "Germany",
note = "8th IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2013 ; Conference date: 17-06-2013 Through 20-06-2013",
}