Section: New Results

NGS methodology

Participants : Dominique Lavenier, Claire Lemaitre, Pierre Peterlongo, Guillaume Rizk, Anaïs Gouin, Fabrice Legeai.

• Efficient Kmer counting: Counting all the substrings of length k (k-mers) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of distinct k-mers to count. We have developed a new streaming algorithm for that purpose which only requires a fixed user-defined amount of memory and disk space. This approach realizes a memory, time and disk trade-off. DSK is the first approach that is able to count all the 27-mers of a human genome dataset using only 4.0 GB of memory and moderate disk space (160 GB), in 17.9 h. DSK can replace a popular k-mer counting software (Jellyfish) on small-memory servers. [24]

• Questionning the classical re-sequencing analyses approach: Classical re-sequencing analyses are based on a first step of read mapping, then only mapped reads are taken into account in following analyses such as variant calling. We investigated the sources of unmapped reads in aphid re-sequencing data of 33 individuals, and we demonstrated that these reads contain valuable information that should not be discarded as usually done in such analyses. We proposed also an approach to extract this information, based on assembly and re-mapping. [34]

• Repeat detection A new algorithm was developed for detecting long similar fragments occurring at least twice in a set of biological sequences. The problem becomes computationally challenging when the frequency of a repeat is allowed to increase and when a non-negligible number of insertions, deletions and substitutions are allowed. The proposed algorithm, called Rime (for Repeat Identification: long, Multiple, and with Edits) performs this task, and manages instances whose size and combination of parameters cannot be handled by other currently existing methods. To the best of our knowledge, Rime is the first algorithm that can accurately deal with very long repeats (up to a few thousands), occurring possibly several times, and with a rate of differences (substitutions and indels) allowed among copies of a same repeat of 10-15% or even more. [17]