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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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Long read as input #108

Closed AmaliT closed 4 years ago

AmaliT commented 4 years ago

Hi

I was wondering if it would be possible to use long reads (such as output from ONT/Pacbio) on novoplasty tool as SE input? Thoughts?

Cheers Amali

ndierckx commented 4 years ago

Hi,

No that won't work, the error profile is too different and the read lengths vary too much.

Greets

jdmontenegro commented 4 years ago

what about corrected long reads or HiFi reads?

ndierckx commented 4 years ago

If the reads have around the same length it could maybe work, but I am sure there are better assemblers available for long reads...

jdmontenegro commented 4 years ago

I was more concerned about the assembler being aware of circular contigs. I am not aware of many long read assemblers that are also capable of handling circular genomes. Any suggestions are more than welcome.

Cheers,

Juan D. Montenegro

El sáb., 11 ene. 2020 5:17 p. m., Nicolas Dierckxsens < notifications@github.com> escribió:

If the reads have around the same length it could maybe work, but I am sure there are better assemblers available for long reads...

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ndierckx commented 4 years ago

If just started working with long read data recently, so I don't have much experience with it. But the complete organelle genome should be assembled in one contig I think, it can't be that complicated to assemble it with long reads. Did you already tried for your dataset with long read assemblers (and is it for chloroplasts or mitochondrial genomes?)

jdmontenegro commented 4 years ago

Well,

I have only tried flye assembler and is producing two non-overlapping contigs. It looks like. A pretty decent result, but I would like to find the reads joining both ends of the contigs, but I cannot find them, so cannot put them together in a single contig.

I have not tried canu or Falcon on this data yet, but I have not found any obvious reference that it supports circularization. Perhaps that's something I need to look in the assembly graph rather than the final assembly.

Thank you Anyway.

Cheers,

Juan D. Montenegro

El dom., 12 ene. 2020 4:12 p. m., Nicolas Dierckxsens < notifications@github.com> escribió:

If just started working with long read data recently, so I don't have much experience with it. But the complete organelle genome should be assembled in one contig I think, it can't be that complicated to assemble it with long reads. Did you already tried for your dataset with long read assemblers (and is it for chloroplasts or mitochondrial genomes?)

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ndierckx commented 4 years ago

You could align all the long reads to those two contigs, maybe some reads that align will overlap, can do that with minimap2