Question: Pac bio assembler
1
gravatar for mustafa_aljadi
6 weeks ago by
mustafa_aljadi10 wrote:

Hi All, I have a PacBio raw data I want to assemble, what is the list of good assembler to assembler available? Thanks

assembly • 162 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by mustafa_aljadi10
1

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.

ADD REPLYlink written 6 weeks ago by alex.zaccaron200

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

ADD REPLYlink modified 6 weeks ago • written 6 weeks ago by mustafa_aljadi10

No idea if this is any better but from PacBio itself: https://github.com/PacificBiosciences/pb-assembly

ADD REPLYlink written 6 weeks ago by GenoMax96k

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.

ADD REPLYlink written 4 weeks ago by derek.bickhart0

I think Flye is a good one but I have not tested it with Pacbio data.

ADD REPLYlink written 6 weeks ago by juanjo75es80
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