Table 3.
Summary of the number of replicates that were able to generate a complete chromosome with either Flye or Canu (long read data only) or any of the Unicycler parameter sets (short- and long read data) for the nine extraction–purification treatments. There are three extraction methods (EZ1, Qiagen EZ1 DNA Tissue kit; MPIH, in-house variation of Lucigen MasterPure Complete DNA and RNA Purification kit developed at the National Microbiology Laboratory; and QIA, Qiagen DNeasy Blood and Tissue kit) and three purification methods (AMPure, Beckman Coulter AMPure XP Beads; EtOH, ethanol precipitation; and unpurified, no purification)
|
Extraction and purification method |
n |
No. of replicates with complete chromosomes |
||
|---|---|---|---|---|
|
Long read data only |
Short and long read data |
|||
|
EZ1 |
AMPure |
9 |
9 |
9 |
|
EtOH |
9 |
8 |
9 |
|
|
Unpurified |
3 |
3 |
3 |
|
|
MPIH |
AMPure |
9 |
6 |
6 |
|
EtOH |
9 |
5 |
7 |
|
|
Unpurified |
9 |
8 |
9 |
|
|
QIA |
AMPure |
4 |
4 |
4 |
|
EtOH |
4 |
4 |
4 |
|
|
Unpurified |
4 |
4 |
4 |
|
|
TOTALS |
60 |
51 |
55 |
|