run report

[abayega]

Is there a way we can get an output from the run showing things like which contigues were joined, etc. Also, is the analysis done with repeat masking and if not, how can we run it with repeat-masking?

Thanks for the npscarf tool

[hsnguyen]

We indeed output the order of joined contigs in the .japsa file, beside the .fasta file of final assembly. If you want to see the assembly in more details, use the option -v for verbose logging. This option is mainly for debugging and its output is not well-organized but I hope you can find what you need there.

We are not using repeat-masking in our assembly but you can run it on the final assembly (.fasta file) afterward. Feel free to contact us if you have any further questions. Thanks.

[abayega]

Very many thanks for getting in touch with the reply.

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On Tue, Nov 15, 2016 at 11:17 PM -0500, "hsnguyen" notifications@github.com wrote:

We indeed output the order of joined contigs in the .japsa file, beside the .fasta file of final assembly. If you want to see the assembly in more details, use the option -v for verbose logging. This option is mainly for debugging and its output is not well-organized but I hope you can find what you need there.

We are not using repeat-masking in our assembly but you can run it on the final assembly (.fasta file) afterward.

Feel free to contact us if you have any further questions. Thanks.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.

[abayega]

Hi, kindly help me figure out the file format used in the .japsa output. What do the different fields refer to?

Kind regards

[mdcao]

Hi japsa is just a experimental file format and is not yet stable. Please use fasta file in the meantime.

Minh

On 29 Nov 2016 5:59 AM, "abayega" notifications@github.com wrote:

Hi, kindly help me figure out the file format used in the .japsa output. What do the different fields refer to?

Kind regards

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[abayega]

Hi, I really need your assistance here. We used npscarf to do gapclosing and contig joining and the results looked super good, but we want to be sure its not an artificat. We had an in-house assembly of total length 430Mb, 15,300 contigs. After using 0.5X coverage of Nanopore reads the number of contigs reduced to 1,600, and the N50 increased by ~1Mb. From your experience is this reasonable or is it some artificat? Thanks

On Monday, November 28, 2016 4:37 PM, Minh Duc Cao <notifications@github.com> wrote:

Hi japsa is just a experimental file format and is not yet stable. Please use fasta file in the meantime.

Minh

On 29 Nov 2016 5:59 AM, "abayega" notifications@github.com wrote:

Hi, kindly help me figure out the file format used in the .japsa output. What do the different fields refer to?

Kind regards

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[mdcao]

Hi there,

Great to hear you find npScarf useful. In our experience, that is mostly correct. Of course, there might be some artifacts from alignment false positives (bwa mem) and these will be automatically corrected with more data. I would say the results you have is the best one could get from .5X fold coverage.

We would be more happy to give you more support if you could contact us via email to s.hoangnguyen@imb.uq.edu.au and m.cao1@uq.edu.au.

We also have an improved version of npScarf, but it is not yet stable to be documented in github. Once we know your problem better, we could tailor that to your genome.

Cheers Minh

On 29/11/16 09:22, abayega wrote:

Hi, I really need your assistance here. We used npscarf to do gapclosing and contig joining and the results looked super good, but we want to be sure its not an artificat. We had an in-house assembly of total length 430Mb, 15,300 contigs. After using 0.5X coverage of Nanopore reads the number of contigs reduced to 1,600, and the N50 increased by ~1Mb. From your experience is this reasonable or is it some artificat? Thanks

On Monday, November 28, 2016 4:37 PM, Minh Duc Cao notifications@github.com wrote:

Hi japsa is just a experimental file format and is not yet stable. Please use fasta file in the meantime.

Minh

On 29 Nov 2016 5:59 AM, "abayega" notifications@github.com wrote:

Hi, kindly help me figure out the file format used in the .japsa output. What do the different fields refer to?

Kind regards

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/mdcao/npScarf/issues/8#issuecomment-263377147, or mute the thread

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