I wanted to know the best method/pipeline for gene annotation after draft genome assembly for gene annotation. Using BLAST is one way to go. Is there any tool (with good accuracy) that can annotate the genome??
Thank you in advance.

(My draft assembly is done using Masurca and SPades with paired-end reads, mate-pair reads and pacbio reads.)

I am assuming this is a Eukaryotic species. Depending on the specific species, you could use related-species' protein evidence as input along with a BUSCO-trained custom Augustus species and MAKER (http://www.yandell-lab.org/software/maker.html) to predict protein-coding genes. If there is a related, well-annotated species (ideally from ENSEMBL), you could use the Comparative Annotation Toolkit (CAT, https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit). You could also run MAKER first and then align the **predicted cDNA transcripts** to your de novo genome and use that as input for Augustus PB in the CAT workflow.

edit: changed predicted proteins to cDNA transcripts