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ndierckx / NOVOPlasty

NOVOPlasty - The organelle assembler and heteroplasmy caller
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non-standard base calls in front of outcome contigs #167

Open commang1 opened 3 years ago

commang1 commented 3 years ago

Hi, and thank you for sharing your code here. It having been great help for our work.

I have noticed some of the outcome contigs contain non-standard base calls in the beginning of the sequence. I also found same problem with other organisms, such as algae Is there any way to prevent the cause of the problem?

One more thing, I've tried to run it with the newest version, NOVOPlasty4.2, and failed to assemble due to out of memory even though I didn't set a max memory usage.

version used : NOVOPlasty 2.6.7 sample used for : Thalassia testudinum

Chloroplasty assembly outcome :

Contig07+c22380_c22313_c22292_c22380_c22313_c22292_c22161_c22094_c22073_c21942_c22094_c22073_c21875_c21729_c21662_c21729_c21662_c1872_064943071 TKWATSRAWKTSTTYMMGWTCTTCCCTTTCTTCCTCGTTTTCGGAATCCATCCCTTCCTC

Contig09+c22380_c22313_c22292_c22380_c22313_c22292_c22161_c22094_c22073_c21942_c22094_c22073_c21875_c21729_c21662_c21729_c21662_c1872_64943071 TKWATSRAWKTSTTYMMGWTCTTCCCTTTCTTCCTCGTTTTCGGAATCCATCCCTTCCTCTTCTG

ndierckx commented 3 years ago

These ambiguous nucleotides, it means the exact nucleotide can be determined, they are standard in these situations. Probably very low quality or coverage in that region.

Can you send me the log file of version 4.2? Have you also updated to the latest config file?

commang1 commented 3 years ago

Thank you for your response. I'll run another assembly with the same organelle on two different versions (2.6.7 and 4.2) and will let you know.

On Mon, Mar 1, 2021 at 2:14 PM Nicolas Dierckxsens notifications@github.com wrote:

These ambiguous nucleotides, it means the exact nucleotide can be determined, they are standard in these situations. Probably very low quality or coverage in that region.

Can you send me the log file of version 4.2? Have you also updated to the latest config file?

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