PT  - JOURNAL ARTICLE
AU  - Pei Wu
AU  - Chao Liu
AU  - Ou Wang
AU  - Xia Zhao
AU  - Fang Chen
AU  - Xiaofang Cheng
AU  - Hongmei Zhu
TI  - AsmMix: A pipeline for high quality diploid <em>de novo</em> assembly
AID  - 10.1101/2021.01.15.426893
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.01.15.426893
4099  - http://biorxiv.org/content/early/2021/01/18/2021.01.15.426893.short
4100  - http://biorxiv.org/content/early/2021/01/18/2021.01.15.426893.full
AB  - In this paper, we report a pipeline, AsmMix, which is capable of producing both contiguous and high-quality diploid genomes. The pipeline consists of two steps. In the first step, two sets of assemblies are generated: one is based on co-barcoded reads, which are highly accurate and haplotype-resolved but contain many gaps, the other assembly is based on single-molecule sequencing reads, which is contiguous but error-prone. In the second step, those two sets of assemblies are compared and integrated into a haplotype-resolved assembly with fewer errors. We test our pipeline using a dataset of human genome NA24385, perform variant calling from those assemblies and then compare against GIAB Benchmark. We show that AsmMix pipeline could produce highly contiguous, accurate, and haplotype-resolved assemblies. Especially the assembly mixing process could effectively reduce small-scale errors in the long read assembly.Competing Interest StatementThe authors have declared no competing interest.