Scalable post-assembly editing software for finishing and annotating personal genomes

We are entering a new era of personal genomics where an individualandapos s genome sequence will be used to identify disease susceptibilityimprove diagnosis and better treat illnesses as well as be combined across cohorts and populations to identify new biomarkers and causal mutations underlying any phenotypeDespite the tremendous success of mapping short read next generation sequencingNGSdata onto a reference genomeresequencingin identifying genetic variation in a new genomethe inherent lack of long range connectivity together with reference induced biases make obtaining complete haplotype phased genomes exceedingly difficultEmerging long read technologies are beginning to address this critical shortcoming by direct de novo assembly of an individualandapos s genomeHoweverinitial de novo assemblies typically consist of many thousands of unordered contigs that require extensive post assembly processing to produce finished sequences that can be effectively mined for genetic content and variationThusthere is an urgent need for integratedscalable post assembly software thatautomatically organizesjoins and phases the initial contigs into complete haplotype sequencessupports optional NGS and or manual polishing andprovides initial automated annotation of those sequencesCurrentlysuch software does not exist and instead users must cobble together a confusing array of difficult to usetask specific pieces of open source programsDNASTARandapos s post assembly editing programSeqMan ProSMPhas a proven history in finishing bacterial sized genomes although it currently lacks the scalability and all the needed functionality to tackle human genome sized problemsThe primary goal of this Fast Track proposal is to create a fully scalable version of SMP for the automated finishing and annotation of de novo assembled large eukaryotic genomes while also providing a manual editing platform when neededDuring Phase Iwe will develop two key prototypesa new assembly file formateBAMwhich is interconvertible with the BAM formatbut also is editable like our SQD files anda rapid reference assisted contig scaffolding tool adapted from our proprietary Disk Sort AlignmentDSAalgorithmWith that foundationwe will complete the transformation of SMP in Phase II byrefining the eBAM format for optimal editing performancebuilding a newbit version of the SMP editing engine that incorporates the additional functionality necessary for post assembly finishing of large eukaryotic genomes including automated DSA based scaffolding and phase aware gap fillingcontig joining and haplotype refinementcreating a new DSA based genome aligner for rapidly aligning a finished sequence to an annotated reference genome which together witha new feature transfer and analysis modulewill permit initial annotation of the finished genome along with a cataloging of variants and their impact in both native and reference coordinatesInclusion of the reference coordinates allows variants in the new genome to be easily associated with the wealth of information available through the numerous online knowledgebase resources New advances in DNA sequencing are making it possible to construct the entire genome sequence of every personGleaning the genetic variation unique to each individual from these sequences has tremendous implications for personalized medicineincluding understanding the causes of and cures for human diseaseIn this projectwe will develop the finishing software needed to determine the complete genome sequence as well as its genetic content and variation from any individual