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Old 07-03-2017, 08:56 PM   #1
discoveradnan
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Location: Pakistan

Join Date: Oct 2015
Posts: 23
Default NCBI WGS submission: Need Help

Dear Seniors,
I'm a newbie in field of bioinformatics and learning everything on my own by following tutorials available online. Right now, I'm facing a roadblock in submitting WGS sequences to NCBI. My pipeline for producing scaffold is as follows,
FASTQ files -> Trimmomatic -> SPades -> CONTIGuator

The species I assembled belong to genus:
1)Escherichia
2)Pseudomonas
3)Citrobacter

After submitting the sequences to NCBI, I have been asked following questions and I don't know how to best answer them. For that I need your kind help,

Quote:
"To process the genome, please confirm that these gapped genomes are circular.

If they are not:

[1] Is there also a gap at the end between the last and first base

[2] Was the genome assembly not circularized

[3] Is any possible overlap at the ends was not trimmed.

This information will allow us to process your genome."
What tools I can use to make sure that whether they were circularized by assembler software or not? Also what does they mean by "gap at the end between the last and first base" How can i make sure of that?

I will be really thankful, if you can assist me,

Kind Regards,
Adnan
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assembly, bioinformatics, circularization, denovo, fastq

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