I am quite new in bioinformatics field and especially PACBIO file and their technology. I just want to complete my de novo assembly one new small genome of bacteria. I started to assembly step by step from extract fasta file from .bas.h5 file and then corrected all reads by using PBcR. Now, I want to finish my job by using Quiver to polish it. However, it requires some file that I do not understand and do not know how to get it. That is
.cmp.h5 file which generated by pbalign. In pbalign input requirement, the input reference sequences are required in the parameter to get the result. Here is my question,
1. How can I get that reference sequence to use with my assembly?
2. In this situation, the input reference sequences are not the same reference sequence that use for reference assembly, am I right?
3. How can I calculate PACBIO x coverage? Is that just divide all bases by genome size?
I am really sorry to bother you all guys with my quite naive questions, I really try to find the answer but I can't.
Thank you all :)