HapSolo: an optimization approach for removing secondary haplotigs during diploid genome assembly and scaffolding.

ABSTRACT:

Background

Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary and secondary contigs are not properly identified, the primary assembly will overrepresent both the size and complexity of the genome, which complicates downstream analysis such as scaffolding.

Results

Here we illustrate a new method, which we call HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using a cost function. The cost fun

SUBMITTER: Solares EA 

PROVIDER: S-EPMC7788845 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature