Hi all,
I'm using kSNP to call snps in my data and generate a vcf file of the outcomes.
I have a reference genome which i have used prokka to annotate but i am having trouble integrating this reference to be used.
The contigs of the day zero reference strain were glued together using "merge_contings_fasta" before processing with prokka.
When i examine the files in the output folder, absolutely nothing is mapped to an annotation.
I have just 6 genomes a patient, one of these genomes is a "day zero" strain that has gone in and the other 5 have been pulled out at select intervals. Any variance we see could be a potential adaptation of the bacteria to life inside the host.
I have assembled genomes and reads (fastqs.)
I want to create a vcf file that i can map onto a prokka annotated reference genome.
Has anyone figured out how to do this via kSNP, or can you suggest anything else?
I'm also trying breseq
many thanks
Anish
I'm using kSNP to call snps in my data and generate a vcf file of the outcomes.
I have a reference genome which i have used prokka to annotate but i am having trouble integrating this reference to be used.
The contigs of the day zero reference strain were glued together using "merge_contings_fasta" before processing with prokka.
When i examine the files in the output folder, absolutely nothing is mapped to an annotation.
I have just 6 genomes a patient, one of these genomes is a "day zero" strain that has gone in and the other 5 have been pulled out at select intervals. Any variance we see could be a potential adaptation of the bacteria to life inside the host.
I have assembled genomes and reads (fastqs.)
I want to create a vcf file that i can map onto a prokka annotated reference genome.
Has anyone figured out how to do this via kSNP, or can you suggest anything else?
I'm also trying breseq
many thanks
Anish