JOBIM 2020 Montpellier, 30 juin - 3 juillet Long papers 1 Paper 1 Long-read error correction: a survey and qualitative comparison Pierre Morisse1, Thierry Lecroq2 and Arnaud Lefebvre2 1 Normandie Universit´e,UNIROUEN, INSA Rouen, LITIS, 76000 Rouen, France 2 Normandie Univ, UNIROUEN, LITIS, 76000 Rouen, France Corresponding author:
[email protected] Extended preprint: https://doi.org/10.1101/2020.03.06.977975 Abstract Third generation sequencing technologies Pacific Biosciences and Oxford Nanopore Technologies were respectively made available in 2011 and 2014. In contrast with second generation sequencing technologies such as Illumina, these new technologies allow the se- quencing of long reads of tens to hundreds of kbps. These so-called long reads are partic- ularly promising, and are especially expected to solve various problems such as contig and haplotype assembly or scaffolding, for instance. However, these reads are also much more error prone than second generation reads, and display error rates reaching 10 to 30%, depending on the sequencing technology and to the version of the chemistry. Moreover, these errors are mainly composed of insertions and deletions, whereas most errors are substitutions in Illumina reads. As a result, long reads require efficient error correction, and a plethora of error correction tools, directly targeted at these reads, were developed in the past nine years. These methods can adopt a hybrid approach, using complementary short reads to perform correction, or a self-correction approach, only making use of the information contained in the long reads sequences. Both these approaches make use of various strategies such as multiple sequence alignment, de Bruijn graphs, hidden Markov models, or even combine different strategies.