Comparing the result of the consensus, we found that the result was not identical between viridian and our lab-built ivar pipeline on artic V3 protocol.
With viridia, the low depth of coverage regions were greatly influenced, resulting ambiguities, especially the spike region.
Down here is our depth of coverage plot after filtered out bad reads.
In addition, filtering human read from raw reads would make artifact SNPs from low-frequency alleles.
Our pipeline consists of mapping raw read (bwa-mem) then filtered bad quality reads ( samtools with -bSq 20 flag ). The filtered ones were then trimmed the amplicon primers set (ivar with -e flag). The consensuses were called afterthat.
Comparing the result of the consensus, we found that the result was not identical between viridian and our lab-built ivar pipeline on artic V3 protocol.
With viridia, the low depth of coverage regions were greatly influenced, resulting ambiguities, especially the spike region.
Down here is our depth of coverage plot after filtered out bad reads.
In addition, filtering human read from raw reads would make artifact SNPs from low-frequency alleles.
Our pipeline consists of mapping raw read (
bwa-mem) then filtered bad quality reads (samtoolswith-bSq 20flag ). The filtered ones were then trimmed the amplicon primers set (ivarwith-eflag). The consensuses were called afterthat.