Next-Gen Sequence Analysis in CoGe: Read Alignment, Expression Analysis, SNP Identification, and What's to Come

Next-Gen Sequence Analysis performed by hand is a time-consuming process that requires specialized knowledge of computer hardware and operating systems, as well as an array of disparate bioinformatic software packages.  CoGe's new Next-Gen Sequence Analysis toolkit dramatically simplifies the process by automating workflow generation through an easy-to-use web application. The user is guided through the process of uploading their FASTQ read data to CoGe (via desktop, FTP, or the iPlant Data Store) and provided with a menu of options for read alignment, expression analysis, and SNP identification. Many common third-party bioinformatic tools are available, such as TopHat, HISAT2 and GSNAP for read alignment, Cufflinks for expression analysis, and Platypus and SAMtools for SNP identification.  Analysis results can be viewed in CoGe's genome browser, and optionally shared with other CoGe users.  Future downstream analyses currently under development include diversity quantification, ChIP-seq analysis, and GWAS.