基因组的组装.pdfVIP

denovo Assembly Tissue samples  Plant：Etiolated seedlings, callus, tissue culture, tender leaves.  Animal：Tissues with less fat such as muscles and blood. If the sex determination is XY,XX type is preferable. And ZZ type is better than ZW.  It would be better to provide samples from the same individual. 2 Filter DataFilter Data t n Kmer Analysis e t Error Correction n o Assembly C Assembly Evaluation 3 Filter Data Filter reads with NX percent base is N. Filter reads with many low quality. Filter adapter contamination. (match length=10bp, mismatch=3) Filter PCR duplication. Filter reads with small insertsize. (overlap =10bp, mismatch =10%) 4 Filter Data t n Kmer Analysis e t Error Correction n o Assembly C Assembly Evaluation 5 Kmer Analysis Select Kmer to traverse the entire genome Kmer depth frequency distribution obey Poisson distribution k b G num num k b depth depth Note：knum: The number of Kmers; kdepth :The expected depth of kmers; bnum :The number of bases; bdepth : The expected depth of bases.