Polish_genome

[yao-chenxin]

Hi, author:
I want to polish the assembled genome and then get consensus FASTA, using Merfin. I now have FastA files and Illumina Reads FastQ files; How do I get a VCF file？Is it possible to use GATK to map FASTQ reads to the self-assembled genome FASTA?
Look forward to hearing from you, thanks！
With best wishes.

[arangrhie]

Hello @yao-chenxin , sorry for the very delayed reply.
Yes, you could use GATK or DeepVariant. Up to you.
I assume the assembly wasn't generated from Illumina reads though?

Best,
Arang