Entering edit mode
3.3 years ago
mustafa_aljadi
▴
10
Hi All, I have a PacBio raw data I want to assemble, what is the list of good assembler to assembler available? Thanks
You could provide some details of what you are trying to assemble. There are discussion about it already. Check here, and a (not that recent) review paper here. But Canu is among the top assemblers out there.
I am trying to make an assembly by PAC bio reads of beaver. it's already done by canu but the results weren't good enough. so I am looking for other assemblers that can do the assembly. Also, I am thinking to trim these but I don't know what is a good trimming program for PAC bio reads. Any suggestion, please? Thanks in advance
No idea if this is any better but from PacBio itself: https://github.com/PacificBiosciences/pb-assembly
We've had good success with both Flye and Canu assemblers; however, if your reference animal is highly heterozygous or if your input sequence is highly contaminated, you'll get fairly poor results in your output assembly. Also, lack of sufficient coverage (targets should be > 50X coverage for a diploid, homozygous mammalian genome) can be an issue.
My recommendation is to try using Merqury or KAT to assess the quality of your input sequence reads compared to your assembly. If you notice a huge error band (the leftmost bar) or the lack of het/hom kmer peaks in your kmer spectra plots, then you have some issues with contamination. I'd recommend running reads through Centrifuge or another tool to remove the contamination first before assembling.
I think Flye is a good one but I have not tested it with Pacbio data.