sequenceassemblymanager

sequenceassemblymanager内容摘要：

s Ultracontigs Ultracontigs: Higher Arrangements of Supercontigs based on fingerprint map (clone tilling path) (clone gaps estimated and supercontigs oriented Genomic DNA libraries (plasmid, fosmid, BAC) Phrap Arachne InHouse SAM Database Glimmer Arachne GeneMark Phrap SAM Database MySQL database 37 tables Info stored as follows: System Configuration Directories Filenames Nodes Programs Arguments Input (WGS/Fingerprint) Data Clustering Contig Supercontig Ultracontig Gene Prediction Which context? Which contig? Gene Annotation Blast Interpro Manual Analyses Gaps Overlaps Ties Library Tasks Assembly Summary SAMdb SAM Database Modules (PERL) written for managing DB connection / allow basic read/write interactions with the database Credentials needed to read/write from/to SAMdb is provided: at mand line from web (fairly secure using PERL modules that freezes, presses, encrypts and encodes data) System Core Glimmer Arachne GeneMark Phrap System Core 10 PERL scripts 9 Wrappers (PERL/Shell Script) 11 modules System is designed to use any assembly program and any gene finders as they bee available External program parameters, location, input, output directories are all located in the database (Config table) Typically, configuration information is initially retrieved from SAMdb by head program and passed on. Individual libraries perform set of related task: DB Interaction (basic) XML creation/parsing HTML creation Assembly Parsing Assembly Analysis Gap/Lib/Overlap Encryption Data Manip(WEB) DB dumps User Interface Glimmer Arachne GeneMark Phrap Admin amp。 Collaborators User Interface Read Info (cached nightly, LIMSdependent) Per Library Info (cached nightly, LIMSdependent) Assembly Stats amp。 General Info Sequencing amp。 Assembly Info User Interface Sequencing amp。 Assembly Info User Interface Assembly Analysis Pages: Access preputed data From SAMdb Assembly Analyses User Interface Assembly Analyses User Interface Assembly Analyses Evaluates: Library randomness Bias for specific regions with any of the genomic libraries? User Interface。