sequenceassemblymanager(已修改)
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【正文】 Sequence Assembly Manager Ren233。 Warren January 8th, 2020 A Tool To Manage amp。 View Whole Genome Shotgun (WGS) Sequence Assemblies WGS Sequence Projects @ GSC Rhodococcus sp. RHA1 Cryptococcus neoformans WM276 Abundant aerobic soil bacteria with potential use for bioremediation Capable of degrading polychlorinated biphenyls (PCBs) and other aromatic pounds Produces a number of secondary metabolites that may represent a pharmacological interest Cryptococcus is a ubiquitous human pathogen Leading cause of infectious meningitis Australian environmental strain WM276。 Sister strain to serotype B that caused the outbreak on Vancouver Island infecting 50 immunopetent people Genomic Library Construction High Throughput Sequencing RS001 RM004 Tracking Profiling Processing Base Calling Assembly Assembly Analysis Assembly Annotation Sharing Information Libraryspecific analyses Read distribution Insert Size distribution Gap amp。 Overlap clone identification ... Genome Assembly Project Flow Sequence Finishing Gap closure Quality improvement What Is SAM amp。 Why Using It? Generic platform for manipulating WGS assembly data and data analysis, regardless of input type Execute, View, Analyze, Manipulate WGS assemblies Provide an automated platform for gene prediction and annotation Provide a convenient/easy way to store amp。 access WGS assembly data Eases the use of external programs through web interface Central repository for storing assembly, analysis, annotation amp。 finishing information SAMdb Input Data Trace Archive Fingerprint Map System Core Management tools Analysis tools Parsers (PERL) WEB Interface External Programs GeneFinders Assemblers SAM Components SAM Components Glimmer Arachne GeneMark Phrap Data Input Glimmer Arachne GeneMark Phrap Data Input Two Types of Input: Trace Archive Data Fingerprint Map Data To account for different data sources, XML files are created Sequence db on limsdbm and fingerprint clone flat file are our current sources Additional programs must be written to account for the different sources Those programs are NOT an in
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