基因组组装.pdfVIP

Genome Assembly Part I: Why is it difficult and what are the general strategies Reads from sequencing platform 1. Reads start at random positions on the genome 2. Coverage = (overall reads length) / (genome length) Sequence overlaps are the main foundation for assembly 1. “Real” overlap 2. “False” overlap overlap by coincidence ATTGATC ATTGATC ATTGA ATTGA Assembly difficulty from repeats 1. Repeats in genome might cause mis-assembly Assembly difficulty from repeats 2. Stop before and after repeats to avoid mis-assembly rpt1A I III rpt1B II Assembly difficulty from errors A. False branches shorten segments B. False branches destroy uniqueness General assembly pipeline Reads file Contiging Library Info Contigs Scaffolding Filling gaps Scaffolds Assembly Results General strategies 1. Contig assembling by overlap extend Extend toward one direction by overlapping reads Stop when it branches General strategies 2. Contig assembling with De bruijn Graph GCAAAACACTT… GCA K = 3 CAA AAA AAA AAC Genome Assembly Part II: how to assemb