Next-Gen Sequencing Bioinformatics support文档.pptVIP

Next-Gen Sequencing Bioinformatics SupportGPCL-BAC Rick Jordan, Programmer/Analyst J. Lyons-Weiler, Sci. Director September 26, 2008 Process GPCL-BAC Director Analyst meet w/PI Discuss Data Analysis Needs Study Design PI Decides on Use of BAC or “Go it Alone” “Go It Alone” - data (.sff files) “Use the BAC” data analysis $ estimate annotation, assembly, analysis + data PI reviews Preliminary Research Report w/Analyst After final analysis, PI receives Report Data Often the Analysis will be tailored to the application de novo Analysis Flowchart Image processing Lasergene SeqBuilder Reference sequence e.coli K12 Signal Processing de novo Genome Assembly Two software packages currently used: GS FLX Assembler (Newbler algorithm) Can be used for all experiments Lasergene (SeqMan Pro) Single-end experiments only GS de novo Assembler Input: .sff files and per-base quality scores Output: Consensus sequence, assembled de novo Main processing steps: Identify pairwise overlaps between reads Construct multiple alignments of contigs Generate consensus basecalls of contigs Output contig consensus sequences and quality scores, along with ACE file of multiple alignments and assembly metrics files e.g. Graphic Figure of the Assembly (Lasergene 7.2) GS Reference Mapper Generates the consensus DNA sequence by mapping, or alignment, of the reads to a reference sequence Provides a list of high-confidence mutations (individual bases or blocks of bases that differ between the consensus DNA sequence of the sample and the reference sequence) Genome Annotation (sequence functional classes) Gene annotation with SeqManPro e.g. Diagrams Impacted Pathways e.g. Pathway view e.g. COGS table e.g. Sequencing statistics table Base Caller Metrics Quality Filter Metrics Runtime Metrics Quality measures by region Read lengths by region e.g. Blast results e.g. Predicted nucleotide and protein alignment e.g. Predicted protein alignment Grant Text Next Generation Sequence Bioinformat