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Old 01-30-2016, 05:36 AM   #1
mido1951
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Location: Tunisia

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Default assembly "1D" or "2D" or "1D + 2D"

for assembling reads Minion.
Is it possible to use the reads "2D" + "1D" or only "2D"?
I mean is, we can try to put the "2D" and "1D" in a single file and try to do the assembly?
thanks for your response
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Old 03-10-2016, 05:04 PM   #2
ymc
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It is possible to assemble with only 2D because I did that with PBcR already.

I don't know if there is pipeline supporting 2D+1D.

However, for publication grade assembly, ONT assembly from the current 2D reads is not good enough. You better use PacBio for the time being.
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Old 03-13-2016, 01:32 AM   #3
gringer
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Quote:
However, for publication grade assembly, ONT assembly from the current 2D reads is not good enough. You better use PacBio for the time being.
ONT is novel enough that you don't need a perfect genome to get a publication.

While a low consensus error rate is useful, it's not essential for genome assembly. Many viruses can be "scaffolded" with the MinION by using a single read, and then consensus used to correct the bases. A few bacterial sequences are coming out with single-contig assemblies from nanopore-only reads.
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