基因组测序的原理与方法重点.ppt

Raw sequencing reads pre-processing II Sequencing reads numbers Duplicates detection, regional distribution analysis and trimming Adapter detection and trimming Reads quality analysis and low quality reads filter Average quality density distribution Average quality positional distribution regional distribution F-R correlation GC content-quality correlation Insert length distribution Pipeline raw data pre-process Image analysis and basecalling GOAT pipeline (OLB1.6), CASAVA Quality Control GERALD Summary.htm Lane Lane Yield (kbases) Clusters (raw) Clusters(PF) 1st Cycle Int(PF) % intensity after 20 cycles (PF) %PF Clusters % Align (PF) Alignment Score (PF) %Error Rate (PF) 1 526305 97464 +/- 4878 87676 +/- 9219 75 +/- 21 86.17 +/- 5.25 89.76 +/- 5.95 99.06 +/- 0.25 102.41 +/- 1.62 1.30 +/- 0.22 Fastq and Quality Solexa reads of the Fastq format s_1_1_sequence.txt… @HWI-EAS724_0001:8:32:374:374#0/1 GAGCTGTATATGAATAATAGTTCGTTTTTCATTATCCAAGATGGATCGGTATAAAGTCTGCTAAAATAAAGGTACAACG +HWI-EAS724_0001:8:32:374:374#0/1 fcfcfggdfggggfggggcggggggggfgggggcgggfWgggggggggfgcggdgcgcggggfacbbb][bgcgggggd s_1_2_sequence.txt … @HWI-EAS724_0001:8:32:374:374#0/2 TACCGTTAATAGCAGTAATATCATAATAGTAATAGCATCATAACGGTAGTCCCATAAAAGTGTGTCAGTAGTAGTAGTA +HWI-EAS724_0001:8:32:374:374#0/2 ggggfgggggd_adcggggeggfggeggegf`geececdegggggfegcfegggegggfgac[aced`bd__\_c[[Yb Illumina 1.3 format encodes a Phred quality score from 0 to 40 using ASCII 64 to 104 error probability (p): # for solexa: p = 0.01, Q = 19; p = 0,05, Q = 12.8, p = 0.10, Q = 9.5; # for phred: p = 0.01, Q = 20; p = 0,05, Q = 13, p = 0.10, Q = 10; Questions Genome size estimation methods (K-mer Cov) Assembly optimization (parameters) Assembly evaluation (454_Solexa EST) Unmappable solexa reads reuse (filter-assemble) Scaffolding comparison (ABI BIG Bambus blat)solexa to solid feasible? Assembly assessment (BAC, 3730, necessary ?) Sequencing Strategy for solexa