Pipelines to do MinION sequencing of Zika virus

Overlap Graphs

To prepare libraries for this pipeline:

  1. poretools fasta --type 2D <path/to/base/called/reads/> > <name.fasta>
  2. bwa mem -x on2d <indexed_reference.fasta> <name.fasta> | samtools view -bS - | samtools sort -o <name.sorted.bam> -
  3. samtools depth <name.sorted.bam> > <name.coverage>
    • head <name.coverage> # This finds the name of the 'chromosome'; there may be >1.
  4. awk '$1 == "<chromosomename>" {print $0}' <name.coverage> > chr1.coverage
  5. Repeat for paired library
  6. Fill in and into pool1 and pool2 in depth_coverage.R
  7. Stats acquired using poretools stats <path/to/base/called/reads

Reported p20 and p40 values represent percentage of the Zika genome which has at coverage of at least 20/40 reads, respectively.

Overlap graphs and stats on pass libraries: USVI Library 1

NB01-NB07 Overlap

Complete library
  • p20: 0.9815 (+1%)
  • p40: 0.9758 (+1%)
    • Difference: 1%
Incomplete library
  • p20: 0.9702
  • p40: 0.9671

NB02-NB08 Overlap

Complete library
  • p20: 0.9732 (+13%)
  • p40: 0.9631 (+25%)
    • Difference: 1%
Incomplete library
  • p20: 0.8412
  • p40: 0.7145

NB03-NB09 Overlap

Complete library
  • p20: 0.9191 (+25%)
  • p40: 0.8723 (+37%)
    • Difference: 4%
Incomplete library
  • p20: 0.6571
  • p40: 0.5022

NB04-NB010 Overlap

Complete library
  • p20: 0.9932 (+6%)
  • p40: 0.9925 (+9%)
    • Difference: 0.1%
Incomplete library
  • p20: 0.9384
  • p40: 0.9087

NB05-NB11 Overlap

Complete library
  • p20: 0.9779 (+7%)
  • p40: 0.9749 (+10%)
    • Difference: 0.5%
Incomplete library
  • p20: 0.9066
  • p40: 0.8737

NB06-NB12 Overlap

Complete library
  • p20: 0.0163 (+1%)
  • p40: 0 (+0%)
    • Difference: 1%
Incomplete library
  • p20: 0
  • p40: 0

Overlap graphs and stats on pass libraries: USVI Library 3

NB01-NB07 Overlap

p20: 0.2896 p40: 0.2658

NB02-NB08 Overlap

p20: 0 p40: 0

NB03-NB09 Overlap

p20: 0.0925 p40: 0

NB04-NB10 Overlap

p20: 0.3825 p40: 0.3624

NB05-NB11 Overlap

p20: 0.974 p40: 0.9675

NB06-NB12 Overlap

p20: 0 p40: 0