I am getting different results (number of SNPs and SNP distances) when I run ska distance with .skf files generated using ska fastq and ska fasta, with the same genome database. Specifically, the number of SNPs is greater when I use the fasta option than when I use fastq. I wonder if this is associated with error/variation introduced during the assembly process (reads were trimmed and quality assessed), or is there any other issue to consider.
Hi,
I am getting different results (number of SNPs and SNP distances) when I run ska distance with .skf files generated using ska fastq and ska fasta, with the same genome database. Specifically, the number of SNPs is greater when I use the fasta option than when I use fastq. I wonder if this is associated with error/variation introduced during the assembly process (reads were trimmed and quality assessed), or is there any other issue to consider.
Thanks!