This track shows the amplicons and primers for PCR-based genome amplification schemes. The track contains one subtrack for each sequencing protocol primers set. By configuring the track, one can show or hide each set individually. The primer sets are labeled with the name of the first author of the protocol.
Yale hMPXV Amplicon Scheme (Chen et al 2022): This is a primer set for Illumina sequencers,
it was tested on a MiSeq with 2x150nt read lengths.
It is available from Protocols.io.
Based on initial validation, the
approach shows notably higher depth and breadth of coverage across the genome,
particularly with higher PCR cycle threshold (Ct) samples, as compared to
metagenomic sequencing. The average amplicon size is ~2.5kB.
As the primers were designed for the pre-outbreak sequence MT903345, there
is one single mismatch in the genome, for MPXV_102. Its left primer is cagcgtgtataggatggTgacg but the genome is cagcgtgtataggatggCgacg.
Genomic locations of the amplicons are highlighted. Thick rectangles indicate the primers, intervening amplicon sequence is shown with lines and arrows. A click on the amplicons shows both primer sequences.
Primer sequences and names were download from the source publications (Chen et al) and (Welkers et al), aligned to the Rivers reference with our isPcr tool and converted to bigBed with AWK.
The raw data can be explored interactively with the Table Browser or combined with other datasets in the Data Integrator tool. For automated analysis, the genome annotation is stored in a bigBed file that can be downloaded from the download server.
Annotations can be converted from binary to ASCII text by our command-line tool bigBedToBed. Instructions for downloading this command can be found on our utilities page. The tool can also be used to obtain features within a given range without downloading the file, for example:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/mpxvRivers/pcrAmplicon/pcrAmplicon.bb -chrom=NC_063383.1 -start=0 -end=100000 stdout
Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.
Chen NFG et al Monkeypox virus multiplexed PCR amplicon sequencing Protocols.io V2 July 26, 2022
Welkers M et al Monkeypox virus whole genome sequencing using combination of NextGenPCR and Oxford Nanopore Protocols.io V1, July 12, 2022