Motivation RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterise the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available. Current methods for assembling viral quasispecies are either based on overlap graphs or on de Bruijn graphs. Overlap graph based methods tend to be accurate but slow, whereas de Bruijn graph based methods are fast but less accurate. Results We present viaDBG, which is a fast and accurate de Bruijn graph based tool for de novo assembly of viral quasispecies. We first iteratively correct sequencing errors in the reads, which allows us to use large k-mers in the de Bruijn graph. To incorporate the paired-end information in the graph, we also adapt the paired de Bruijn graph for viral quasispecies assembly. These features enable the use of long range information in contig construction without compromising the speed of de Bruijn graph based approaches. Our experimental results show that viaDBG is both accurate and fast, whereas previous methods are either fast or accurate but not both. In particular, viaDBG has comparable or better accuracy than SAVAGE, while being at least nine times faster. Furthermore, the speed of viaDBG is comparable to PEHaplo but viaDBG is able to retrieve also low abundance quasispecies, which are often missed by PEHaplo. Availability viaDBG is implemented in C ++ and it is publicly available at https://bitbucket.org/bfreirec1/viadbg. All data sets used in this article are publicly available at https://bitbucket.org/bfreirec1/data-viadbg/. Supplementary information Supplementary data are available at Bioinformatics online.

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Hematology has become important for making clinical diagnoses in snakes because maintenance techniques in captivity have been improving and increasing their life expectancy. The emergence of diseases in captivity requires the creation of parameters to understand the species in their healthy state. The possible association between the onset of neoplasia, immunosuppression, and viral infection are also important factors to consider. Thus, hematology is a fundamental tool for observing the responses of animals to diseases and treatments. The present study aims to study hematology between two species of snakes and compare the profiles observed with published results. Blood samples were collected from 16 male and female snakes: seven Corallus hortulanus from the family Boidae and nine Python bivittatus from the family Pythonidae belonging to the Biological Museum of the Butantan Institute, São Paulo, Brazil. Complete blood count results including blood smear, total erythrocyte count, leukocytes, and differential leukocyte count were evaluated. The data obtained in this study could help with the diagnosis, the treatment of snakes in captive conditions and in of nature conservation programs.

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