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add time and memory footprint
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HongzheGuo committed Jul 18, 2016
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Expand Up @@ -10,58 +10,39 @@ deBGA is mainly designed by Bo Liu and developed by Hongzhe Guo in Center for Bi
###Memory requirement
The memory usage of deBGA can fit the configurations of most modern servers and workstations. Its peak memory footprint depends on the length of reference genome, i.e., 69.55 Gigabytes and 5.20 Gigabytes respectively for the real H. Sapiens and E. Coli genomes, on a server with Intel Xeon CPU at 2.00 GHz, 1 Terabytes RAM running Linux Ubuntu 14.04.
The wall time and memory footprint of the index construction for the references (the k-mer size of the index is 22) is as follows. The time is in seconds, and the memory footprints are in Gigabytes.
```
No. Reference Time Memory
No. Reference Time Memory
1 E. coli K-12 MG1655 substrain 21 2.02

2 10 E. coli strains 116 3.02

3 20 E. coli strains 200 3.02

4 40E. coli strains 280 4.03

5 62E. coli strains 729 5.04

6 A. thaliana reference genome (TAIR10) 972 7.05

7 19 A. thaliana strains 4993 11.09

8 RefSeq bacteria genomes 69912 153.30

9 xenograft model (hg19+MM10) 42851 130.03

10 human reference genome (hg19) 15786 69.55

```

The memory footprint of deBGA when aligning the reads from the listed datasets (the alignment is conducted with the default setting of deBGA) is as follows. The memory footprint are in Gigabytes.

```
No. Dataset Memory
1 E. coli Sim-62 9.07
1 E. coli Sim-62 9.07
2 ERR008613 9.07

3 SRR522163 9.07

4 SRR530851 9.07

5 A. thaliana Sim-19 12.1

6 Meta Sim 80.64

7 Xenograft Sim 60.48

8 Meta Pseudo-real 80.64

9 H. sapiens Sim-100 40.32

10 H. sapiens Sim-250 40.32

11 ERR174324 40.32

12 Hiseq X Ten: NA12878_L3 40.32

13 ERR161544 40.32

```

###Installation
Current version of deBGA needs to be run on Linux operating system.
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