what is the next step of my NGS data?

Question

[jjeangoh]

Hi! I'm new and currently doing masters in bioinformatics. My DNA data is sequenced using PacBio sequencing. I used MECAT to assemble my DNA data which the output consists of 800 contigs, 51% GC content, 54Mbp (validation by using QUAST). What is the next step? Do I need to combine my contigs into scaffold? Is there any software (for annotation) for PacBio analysis besides software provided by PacBio? Thanks!

[Medhat]

Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone

Answer 1

[Tm]

Yes you can go for scaffolding followed by gap-filing if any gaps are present and then polishing of assembly. There are number of tools for available for these processes, you can use Single Molecular Integrative Scaffolding (SMIS) pipeline followed by pb-jelly and Arrow respectively.

Alternatively, you can go through this paper which is very nice to have good understanding of long read analysis.