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,
"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."
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."
I will be really thankful, if you can assist me,
Kind Regards,
Adnan