Commit 56cc22bf authored by Aaron Petkau's avatar Aaron Petkau

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A number of datasets have been used to benchmark the runtime, memory, and disk usage of SNVPhyl across a range of scenarios using the Docker version of SNVPhyl on a 16-core machine. The results are presented in the table below.
| Case | # Genomes | Read size <br/> (GB) | Runtime <br/> (hrs) | Max Mem. (RSS)<br/> (GB) | Max Mem. (All)<br/> (GB) | Disk Space <br/> (GB) |
| Case | # Genomes | Total read size <br/> (GB) | Runtime <br/> (hrs) | Max Mem. (RSS)<br/> (GB) | Max Mem. (All)<br/> (GB) | Disk Space <br/> (GB) |
|:----------------|:---------:|:--------------------:|:-------------------:|:------------------:|:-------------------:|:---------------------:|
| Docker only | - | - | - | 0.662 | 1.15 | 2.4 |
| Simulated data | 4 | 1.4 | 0.261 | 3.04 | 9.90 | 6.8 |
......@@ -10,7 +10,7 @@ A number of datasets have been used to benchmark the runtime, memory, and disk u
| *S.* Heidelberg | 59 | 40 | 3.04 | 4.07 | 21.4 | 66.6 |
| *S. pneumoniae* | 189 | 169 | 8.23 | 12.4 | 21.7 | 136 |
The **Docker only** case represents the resource useage of the `snvphyl-galaxy` Docker image alone, without any data. The next three cases are data analyzed in the [SNVPhyl manuscript][]. The **Simulated data** case was run using a set of simulated reads through SNVPhyl, based off of *E. coli* str. Sakai (NC_002695) and two plasmids (NC_002128 and NC_002127). The **SNV density filtering** case was run using a set of 11 *Streptococcus pneumoniae* genomes through SNVPhyl. The **_Salmonella_ Heidelberg** case was run using a set of 59 *Salmonella* Heidelberg genomes. The final case was not analyzed in the SNVPhyl manuscript, but consists of a set of 189 *Streptococcus pneumoniae* genomes analyzed in <http://www.ncbi.nlm.nih.gov/pubmed/24957517>. Additional details on this dataset are provided below.
The **Docker only** case represents the resource useage of the snvphyl-galaxy Docker image alone, without any data. The next three cases are data analyzed in the [SNVPhyl manuscript][]. The **Simulated data** case was run using a set of simulated reads through SNVPhyl, based off of *E. coli* str. Sakai (NC_002695) and two plasmids (NC_002128 and NC_002127). The **SNV density filtering** case was run using a set of 11 *Streptococcus pneumoniae* genomes through SNVPhyl. The **_Salmonella_ Heidelberg** case was run using a set of 59 *Salmonella* Heidelberg genomes. The final case was not analyzed in the SNVPhyl manuscript, but consists of a set of 189 *Streptococcus pneumoniae* genomes analyzed in <http://www.ncbi.nlm.nih.gov/pubmed/24957517>. Additional details on this dataset are provided below.
All datasets were run using the default SNVPhyl parameters on a 16-core Intel Xeon CPU (W5590) @ 3.33 GHz with 24 GB of RAM. Additional details on the methods used to run SNVPhyl for each case can be found [here][methods].
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