Arthropod Genome and Transcriptome Assembly and Annotation Utilizing iPlant Resources

Next gen sequencing has brought an enormously informative, but demanding new technology to the doorsteps of life sciences researchers, including those studying arthropods. Arthropod genomics studies often start with a new genome sequence and a broad snapshot of the transcriptome for the organism. These new sequence assemblies are established through a careful series of steps that require software that is difficult to install, may need a large compute capacity and large amounts of ram. The newly-formed iArthropod, under the aegis of iPlant, will be working with members of the arthropod research community to deliver the bioinformatics resources needed for the i5k project, including access to both the servers and the software in a user-friendly form. General needs targeted will include read cleanup, assembly, gene finding, annotation, ortholog resolution, phylogenetic comparison, RNASeq, SNP analysis, and submission to NCBI and other data banks. Special implementations of Maker and WebApollo will be made available. Most of the needed tools are available as Apps in iPlant’s Discovery Environment or Atmosphere now, but others will be established with the participation of the arthropod research community.