Table 1 Comparison of the time of execution for the paired end reads (SRR1027730) using TopHat and PVT pipeline in the host and remote machines respectively
From: PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Steps | TopHat | PVT | ||
|---|---|---|---|---|
Execution Time (mins) | Execution time (mins) in Host machine | Execution time (mins) in Remote machine | Time (mins) considered for PVT of paired end reads | |
Filter_reads | 22 | 21 | - | 21 |
Transfer to remote | Not applicable | 5 | 92* | |
Building Bowtie indices | 6 | 6 | ||
Gene_align | 83 | 42(L) | 37(R) | |
Genome_align | 94 | 39(L) | 41(R) | |
Transfer from remote | Not applicable | 3 | ||
Find_juncs | 12 | 9 | - | 9 |
Transfer to remote | Not applicable | Negligible (~22 s) | 5* | |
Junc_align | 17 | 2(L) | 2(R) | |
Span_reads | 10 | 3(L) | 3(R) | |
Transfer from remote | Not applicable | ~24 s | ||
Report | 40 | 41(L + R) | - | 41 |
Net execution time | 284 | 168 | ||