Safe and complete contig assembly via omnitigs

Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the reads. From the introduction of contigs 20 years ago, assemblers have tried to obtain longer and longer contigs, but the following question was never solved: given a genome graph $G$ (e.g. a de Bruijn, or a string graph), what are all the strings that can be safely reported from $G$ as contigs? In this paper we finally answer this question, and also give a polynomial time algorithm to find them. Our experiments show that these strings, which we call omnitigs, are 66% to 82% longer on average than the popular unitigs, and 29% of dbSNP locations have more neighbors in omnitigs than in unitigs.Comment: Full version of the paper in the proceedings of RECOMB 201

Identification of Variant Compositions in Related Strains Without Reference

Peer reviewe

4Pipe4-A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information

This work was fully supported by projects SOBREIRO/0036/2009 (under the framework of the Cork Oak ESTs Consortium), PTDC/BIA-BEC/098783/2008 and PTDC/AGR-GPL/119943/2010 from Fundação para a Ciência e Tecnologia (FCT) – Portugal. F. Pina-Martins was funded by FCT grant SFRH/BD/51411/2011, under the PhD program “Biology and Ecology of Global Changes”, Univ. Aveiro & Univ. Lisbon, Portugal. D. Batista was funded by FCT grant SFRH/BPD/104629/2014

On Bubble Generators in Directed Graphs

International audienceBubbles are pairs of internally vertex-disjoint (s, t)-paths with applications in the processing of DNA and RNA data. For example, enumerating alternative splicing events in a reference-free context can be done by enumerating all bubbles in a de Bruijn graph built from RNA-seq reads [16]. However, listing and analysing all bubbles in a given graph is usually unfeasible in practice, due to the exponential number of bubbles present in real data graphs. In this paper, we propose a notion of a bubble generator set, i.e. a polynomial-sized subset of bubbles from which all the others can be obtained through the application of a specific symmetric difference operator. This set provides a compact representation of the bubble space of a graph, which can be useful in practice since some pertinent information about all the bubbles can be more conveniently extracted from this compact set. Furthermore, we provide a polynomial-time algorithm to decompose any bubble of a graph into the bubbles of such a generator in a tree-like fashion

A Family of Tree-Based Generators for Bubbles in Directed Graphs

International audienceBubbles are pairs of internally vertex-disjoint (s, t)-paths in a directed graph. In de Bruijn graphs built from reads of RNA and DNA data, bubbles represent interesting biological events, such as alternative splicing (AS) and allelic differences (SNPs and indels). However, the set of all bubbles in a de Bruijn graph built from real data is usually too large to be efficiently enumerated and analysed in practice. In particular, despite significant research done in this area, listing bubbles still remains the main bottleneck for tools that detect AS events in a reference-free context. Recently, in [1] the concept of a bubble generator was introduced as a way for obtaining a compact representation of the bubble space of a graph. Although this generator was quite effective in finding AS events, preliminary experiments showed that it is about 5 times slower than state-of-art methods. In this paper we propose a new family of bubble generators which improve substantially on the previous generator: generators in this new family are about two orders of magnitude faster and are still able to achieve similar precision in identifying AS events. To highlight the practical value of our new generators, we also report some experimental results on a real dataset

Using Minimum Path Cover to Boost Dynamic Programming on DAGs : Co-linear Chaining Extended

Peer reviewe

Development of a set of SNP markers for population genetics of the red gorgonian (Paramuricea clavata), an emblematic species of the Mediterranean coralligenous

Transcriptome sequencing was used for the development of single nucleotide polymorphisms (SNP) for the red gorgonian (Paramuricea clavata). A total of 20,736 SNPs were identified, and 1718 had a coverage of over 100 reads. Of the 480 SNPs tested, 347 SNPs were successfully genotyped at 95 samples from the NW Mediterranean using a MassARRAY System. This set of markers will be of great value for population genetics and phylogeography.Plateforme d'Innovation " Forêt-Bois-Fibre-Biomasse du Futur