Table 2. The computing time required to process the results of human transcriptome analysis using nanopore ONT sequencing technology on Amazon Web Services.
|
№
|
Used configuration and run time (min) |
Procedure |
|||||
|
p3.2xlarge |
p2.xlarge |
t2.xlarge |
t2.2xlarge |
||||
|
Input data size |
|||||||
|
|
37.5GB |
100GB |
37,5GB |
100GB |
100GB |
||
|
1 |
guppy_basecaller |
21 |
60 |
n/d |
error |
n/d |
n/d |
|
2 |
MinIONQC.R |
6.45 |
n/d |
3 |
6 |
6.1 |
6.3 |
|
3 |
cat |
0.13 |
n/d |
4 |
6 |
0.36 |
0.23 |
|
4 |
minimap2 |
8 |
n/d |
4.44 |
11 |
8.7 |
8.3 |
|
5 |
samtools |
0.45 |
n/d |
0.12 |
1 |
0,43 |
0.45 |
|
6 |
salmon quant |
13.27 |
n/d |
3.45 |
15 |
error |
13.1 |
|
7 |
Grep* |
|
|
|
|
|
|
|
Overall (min.) |
|
49.3 |
60 |
15.01 |
39 |
16 |
28.38 |
Note. *GPU is required to perform the procedure. **grep "protein_coding" – a command selecting protein-coding genes from the data-counting results. ***The running the "salmon quant" procedure using t2.xlarge configuration caused an error, probably related to insufficient RAM. n\d - the command was not run, error - the command was run, but coused an execution error; or no information in screen output for more than 10 minutes.