Description
This track shows the primers for the
RAPID
SARS-CoV-2 sequencing protocol, also commonly referred to as Midnight.
The primers enable amplification of the genome of SARS-CoV-2.
This approach uses multiplexed 1200 base pair (bp) tiled amplicons. Briefly, two PCR
reactions are performed for each SARS-CoV-2 positive patient sample to be sequenced.
One PCR reaction contains thirty primers that generate the odd numbered
amplicons ("Pool 1"), while the second PCR reaction contains twenty eight primers
that generate the even numbered amplicons ("Pool 2"). After PCR, the two amplicon
pools are combined and can be used for a range of downstream sequencing approaches. Primers
were all designed using Primal Scheme
and described in
Nature Protocols 2017. This primer set results in amplicons that exhibit lower levels of
variation in coverage compared to other commonly used primer sets.
Display Conventions and Configuration
Genomic locations of primers are highlighted. A click on them shows the primer pool.
This is one of the few tracks that may be best displayed in "full" mode.
Methods
RAPID primer sequences were downloaded from the
Google Spreadsheet and converted to bigBed. More
details are available in the paper referenced below or in the
supplemental files on Zenodo.
Data Access
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/wuhCor1/bbi/rapid.bb -chrom=NC_045512v2 -start=0 -end=29902 stdout
Please refer to our
mailing list archives
for questions, or our
Data Access FAQ
for more information.
References
Freed NE, Vlková M, Faisal MB, Silander OK.
Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and
Oxford Nanopore Rapid Barcoding.
Biol Methods Protoc. 2020;5(1):bpaa014.
PMID: 33029559; PMC: PMC7454405
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