Sequence assembly demystified

N Nagarajan, M Pop - Nature Reviews Genetics, 2013 - nature.com
Advances in sequencing technologies and increased access to sequencing services have
led to renewed interest in sequence and genome assembly. Concurrently, new applications …

SNP genotyping and population genomics from expressed sequences–current advances and future possibilities

P De Wit, MH Pespeni, SR Palumbi - Molecular ecology, 2015 - Wiley Online Library
With the rapid increase in production of genetic data from new sequencing technologies, a
myriad of new ways to study genomic patterns in nonmodel organisms are currently …

Analysis of RNA-Seq data using TopHat and Cufflinks

S Ghosh, CKK Chan - Plant Bioinformatics: Methods and Protocols, 2016 - Springer
The recent advances in high throughput RNA sequencing (RNA-Seq) have generated huge
amounts of data in a very short span of time for a single sample. These data have required …

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

DR Rokyta, AR Lemmon, MJ Margres, K Aronow - BMC genomics, 2012 - Springer
Background Snake venoms have significant impacts on human populations through the
morbidity and mortality associated with snakebites and as sources of drugs, drug leads, and …

Evaluation of de novo transcriptome assemblies from RNA-Seq data

B Li, N Fillmore, Y Bai, M Collins, JA Thomson… - Genome biology, 2014 - Springer
De novo RNA-Seq assembly facilitates the study of transcriptomes for species without
sequenced genomes, but it is challenging to select the most accurate assembly in this …

Transcriptome Analysis Reveals a Rich Gene Set Related to Innate Immunity in the Eastern Oyster (Crassostrea virginica)

L Zhang, L Li, Y Zhu, G Zhang, X Guo - Marine biotechnology, 2014 - Springer
As a benthic filter-feeder of estuaries, the eastern oyster, Crassostrea virginica, faces
tremendous exposure to microbial pathogens. How eastern oysters without adaptive …

Assessing De Novo transcriptome assembly metrics for consistency and utility

ST O'Neil, SJ Emrich - BMC genomics, 2013 - Springer
Background Transcriptome sequencing and assembly represent a great resource for the
study of non-model species, and many metrics have been used to evaluate and compare …

Optimized deep-targeted proteotranscriptomic profiling reveals unexplored Conus toxin diversity and novel cysteine frameworks

V Lavergne, I Harliwong, A Jones… - Proceedings of the …, 2015 - National Acad Sciences
Cone snails are predatory marine gastropods characterized by a sophisticated venom
apparatus responsible for the biosynthesis and delivery of complex mixtures of cysteine-rich …

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

A Riesgo, SCS Andrade, PP Sharma, M Novo… - Frontiers in …, 2012 - Springer
Introduction Traditionally, genomic or transcriptomic data have been restricted to a few
model or emerging model organisms, and to a handful of species of medical and/or …

De Novo Sequencing and Transcriptome Analysis of the Central Nervous System of Mollusc Lymnaea stagnalis by Deep RNA Sequencing

H Sadamoto, H Takahashi, T Okada, H Kenmoku… - 2012 - journals.plos.org
The pond snail Lymnaea stagnalis is among several mollusc species that have been well
investigated due to the simplicity of their nervous systems and large identifiable neurons …