SNIC
SUPR
SNIC SUPR
DWV, EBV, densovirus genome assembly
Dnr:

SNIC 2018/8-35

Type:

SNAC Small

Principal Investigator:

Joachim Rodrigues de Miranda

Affiliation:

Sveriges lantbruksuniversitet

Start Date:

2018-02-01

End Date:

2019-02-01

Primary Classification:

10606: Microbiology (medical to be 30109 and agricultural to be 40302)

Webpage:

Allocation

Abstract

1. The biological background is the re-sequencing of two strains of a bee virus (DWVuk, DWVebv) from PCR amplicons and the assembly of densovirus sequences from two complex DNA samples, from cricket faeces. 2. DWV sequences: two samples, each consisting of several pooled PCR amplicons of 1-2kb each. Densovirus sequences: two samples of cricket poop DNA: one known to contain densovirus DNA, the other may/maynot contain a distinct densovirus; this is a discovery part of the project. 3. The sequencing data for all samples is from a single, barcoded PacBio run. Particularly for the DWV amplicons there should be a large excess of data. 4. The PacBio reads should first be converted into consensus sequences before subsequent analysis. 5. The DWV amplicons should be aligned to the DWV reference sequences, with SNP calling for all nucleotide bases/deletion at every mapped position, given as a proportion. 6. The densovirus sequences should be assembled, aligned to the reference sequence and a consensus sequence obtained. For the unknown densovirus sample, the assembly/alignment should perhaps be done at amino acid level, in case the putative densovirus is too diverged from the reference sequence for nucleotide-based alignment.