Hi all, I hope the community here can provide some suggestions and solutions for me.

I am doing a fungal genome de novo assembly. Now, I have that fungal sequenced by PacBio and result in three types of sequences

1. CCS sequencing (bam and fastq file)
2. CLR sequencing (only have bam file)
3. CLR_CCS sequencing (only have bam file): followed CCS sequencing using the same sample after the CLR sequencing

I have two questions here. Can I use all three sequences together at the same time to get a better assembly? I think CLR sequences may play a role like the. reference genome when doing the alignment. Since I only have the bam file for #2 and #3, can I transfer the bam file to fastq and then do the assembly (using all three sequences together)?

If someone can provide with the reference, will be awesome.

Appreciated!!!