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2.8 years ago
I have hifiasm assembled contigs from pacbio. These are long single-end reads from extracted plant DNA, I want to align these to my reference sequence to get contiguous scaffold which I could annotate by Augustus. Does anyone know the tools to make scaffold from pacbio sequence contigs?
I dont think your sequencing technology really matters for reference based scaffolding so you could try any tool like ragoo.
It requires just your reference assembly and your assembly contigs. But be sure to check by dotplot afterwards as sometimes it can over scaffold at the ends
I had 1200 contigs from my intial pacbio hifiasm, I aligned it with minimap2 against a reference and then removed all the unaligned reads and sorted it according to the reference.
Now I have a sorted fasta file along with its bam file with 1200 contigs. I believe there are duplication in the contigs. Is this scaffolding will remove those duplicates as well?
If I remember correctly, ragoo was still over-scaffolding in this sense too, adding haplotype phased contigs to the same chromosome...It will perhaps be obvious by dotplot if it does do that for you. If that is the case you could try purging the haplotigs beforehand. There are tools for that.
Yeah, the dot plot also shows these haplotype contigs. Can you recommend tools to purge these haplotigs.