Zika virus sequencing from Florida
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alignments
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README.md

README.md

Data

Sequences | Alignments | Trees | BAMs

Samples

Scripps ID Patient ID Sample type Quality score % Coverage Location of infection
FL001Sa 001 Saliva *** 99.71 Martinique
FL008U 008 Urine *** 90.07 Puerto Rico
FL010U 010 Urine **** 97.69 USA: Florida
FL016U 016 Urine *** 99.88 Puerto Rico
FL021U 021 Urine *** 97.45 USA: Florida
FL022U 022 Urine *** 97.77 USA: Florida
FL030U 030 Urine *** 99.75 USA: Florida
FL032U 032 Urine *** 99.75 USA: Florida
FL036Se 036 Serum *** 99.73 USA: Florida
FL038U 038 Urine *** 99.76 USA: Florida
FL039U 039 Urine **** 99.75 USA: Florida
Hu0015Sa Hu0015 Saliva *** 99.75 USA: Florida
FL01M 7501 Mosquito **** 99.75 USA: Florida
FL02M 7719 Mosquito **** 99.74 USA: Florida
FL03M 7727 Mosquito **** 99.83 USA: Florida
FL04M 16-10416 Mosquito **** 99.72 USA: Florida
FL05M 16-3125 Mosquito **** 99.74 USA: Florida
FL06M Mosquito **** 99.71 USA: Florida
FL08M pool#8 Mosquito **** 97.70 USA: Florida
ZC188Se 423568715 Serum **** 98.26 Columbia
ZC192Se 423401315 Serum **** 98.36 Columbia
ZC204Se 424439915 Serum **** 99.74 Columbia
ZC207Se 423217515 Serum **** 96.68 Columbia
ZC199Se 4238001315 Serum *** 97.44 Columbia

Quality

**** Complete coding sequence, no apparent contamination in aligned bam file
*** Complete coding sequence, some contamination in aligned bam file (confident in consensus)
**  Partial coding sequence, no apparent contamination in aligned bam file
*   Partial coding sequence, some contamination in aligned bam file

Sequencing

  • Library construction was performed using an amplicon-based approach amplicon-based approach.
  • Sequencing was performed on the MiSeq.

Coding-complete genomes

  • Downloaded from NCBI, ViPR, and NextStrain. Only new genomes are added to later folders.
  • Consensus sequences sequenced in our lab are added to the root of the 'consensus_sequences' folder.

Alignments

  • Created using MAFFT.
  • Trimmed to just contain the ORFs.

Maximum likelihood trees

  • Created using the fast algorithm in RAxML using 200 bootstraps.
  • Orange = travel-associated cases; Red = local transmissions.
  • We root trees on KX447517 from French Polynesia.

Time-scaled trees

  • Made with BEAST using the following parameters:
    • Uncorrelated relaxed clock with lognormal distribution, CTMC rate prior.
    • HKYΓ substitution model with codon partitioning.
    • SkyGrid, 50 parameters, time at last point = 4.
    • 30,000,000 states.

Disclaimer. Please note that this data is still based on work in progress and should be considered preliminary. If you intend to include any of these data in publications, please let us know – otherwise please feel free to download and use without restrictions. We have shared this data with the hope that people will download and use it, as well as scrutinize it so we can improve our methods and analyses. Please contact us if you have any questions or comments – we’ll buy beers for #ResearchParasites that spot flaws and faults in the data and come up with improvements!