Author: Jiao Chen; Jiayu Shang; Jianrong Wang; Yanni Sun
Title: A binning tool to reconstruct viral haplotypes from assembled contigs Document date: 2019_7_16
ID: 2basllfv_4
Snippet: Reconstructing the genome-scale strain sequences inside quasispecies is often referred to as genome-scale haplotype reconstruction, where the genomes of strains are called haplotypes. The goal is to assemble short reads from sequenced viral populations into correct haplotype sequences. When the reference genome is available, read mapping can be conducted first to identify local mutations and then cluster the local mutations (or short contigs) int.....
Document: Reconstructing the genome-scale strain sequences inside quasispecies is often referred to as genome-scale haplotype reconstruction, where the genomes of strains are called haplotypes. The goal is to assemble short reads from sequenced viral populations into correct haplotype sequences. When the reference genome is available, read mapping can be conducted first to identify local mutations and then cluster the local mutations (or short contigs) into genome-scale haplotypes. When quality reference genomes are not available, which is often the case for emerging viruses such as SARS coronavirus, read mapping is not a very effective strategy to identify all mutations. Thus, de novo assembly is needed to stitch the reads into haplotypes.
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