I've just uploaded a preprint to bioRxiv (http://www.biorxiv.org/content/early/2017/08/16/177253) that describes the Oyster River Protocol. In short, the protocol user a multi-assembler and multi-kmer approach to generating transcriptome assemblies. Because each individual assembler carries with it biases, leveraging multiple assemblers each of which complement the other results in a really great assembly. The users guide is here: http://oyster-river-protocol.readthedocs.io/en/latest/
To benchmark the protocol, I used 15 publicly available RNAseq datasets of different sizes. All were eukaryotes. Here are the highlights.
Dr. Matt MacManes is looking for a postdoctoral scholar to carry out research associated with a project focused on the genetic underpinnings of color pattern evolution in a mimetic radiation of poison frogs in Peru (see abstract below). The position would begin in the summer/fall of 2017, and be located at the University of New Hampshire. Desirable qualifications for this position include experience with modern approaches in genomics, and bioinformatics. Experience working on questions related to evolution is a plus. We encourage applications from minorities and under-represented groups of all kinds. Please email with questions, and if applying, include details about relevant experience, explaining your interest in the position, as well as a current CV, to Matt ( Matthew.MacManes@unh.edu ). Of note, Kyle Summers is looking for a PHD student to work on this same project - see http://www.balalab.com/fakenews/phd-position-in-the-summers-lab-ecu.
The evolution of color pattern diversity in the context of mimicry has been a focus of theoretical and empirical attention, yet knowledge of the genetic basis of this diversity remains limited. Most work on this topic has focused on a small number of systems (e.g. Heliconius butterflies), limiting the generality of inferences. This proposal combines three research groups with complementary skills and realms of expertise to investigate the genetic basis and population genomic processes underlying color pattern divergence in the context of mimicry in the Peruvian mimic poison frog, Ranitomeya imitator: Dr. Kyle Summers (East Carolina University), Dr. Rasmus Nielsen (UC Berkeley) and Dr. Matthew MacManes (University of New Hampshire). The project focuses on four specific aims: 1. Identify key genetic factors involved in color pattern development in R. imitator by investigating differential gene expression across developmental stages and color pattern morphs. Next generation sequencing will be used to produce developmental stage-specific transcriptomes for each morph, which will be assembled and used to investigate patterns of differential gene expression. 2.Identify the causal gene(s) underlying differences in color pattern between morphs using genome-wide marker arrays (exome capture sequences) to screen transition zone samples and enable admixture mapping. We have identified three admixture zones in the mimetic radiation that will be appropriate for these analyses. 3. Test the association of specific candidate loci with color pattern using pedigree analyses of candidate genes identified from Aims 1 and 2, using a multigenerational pedigree. 4. Test specific hypotheses regarding selection and demographic processes in the transition zones and between mimics and models. These analyses will involve the development of new analytical tools for analyzing selection in admixture zones and targeted sequencing of model species. Together these complementary, mutually reinforcing approaches will begin to reveal the genetic underpinnings and population genomics of color pattern diversity in this mimetic radiation of poison frogs. To summarize, the work proposed here will elucidate the genetic basis of mimetic color pattern diversity in an ecologically relevant context (Mullerian mimicry) that is a central focus of interest in evolutionary biology. By bringing to bear next-generation sequence data, developmental functional genomics, exome capture marker arrays, admixture mapping and population genomic analyses of transition zones, and pedigree analyses, we will investigate the genetic underpinnings of color pattern diversity in this unique mimetic radiation.
PS: Thanks to Chris and Kyle for letting me borrow the text of this advert.
The MacManes Lab is looking for a Masters student to participate in the desert mouse project!