Hi @mobinasri
Really nice job on the HMM_flagger software! I have a quick question regarding its usages on haploid genome assemblies.
I work with Arabidopsis thaliana, which is a model plant species. Arabidopsis is a mostly inbred diploid species which means there is no difference between the two sets of chromosome and therefore no phasing is required.
I have generated long-read genome assembly of an Arabidopsis genotype and since it is 100% homozygous and inbred, the assembly software didnt do any phasing and outputted a single fasta file. Can I still use HMM_flagger to assess this assembly?
In other words, does the tool work when the input behaves as a haploid genome, and could the absence of phasing bias the HMM inference?
Best
Xing
Hi @mobinasri
Really nice job on the HMM_flagger software! I have a quick question regarding its usages on haploid genome assemblies.
I work with Arabidopsis thaliana, which is a model plant species. Arabidopsis is a mostly inbred diploid species which means there is no difference between the two sets of chromosome and therefore no phasing is required.
I have generated long-read genome assembly of an Arabidopsis genotype and since it is 100% homozygous and inbred, the assembly software didnt do any phasing and outputted a single fasta file. Can I still use HMM_flagger to assess this assembly?
In other words, does the tool work when the input behaves as a haploid genome, and could the absence of phasing bias the HMM inference?
Best
Xing