Sample output files

[Csaba Kerepesi]

Here we shared some sample output files of AmphoraNet and then evaluate them.

Bacterial genome:

 - input: Treponema pallidum subsp. pallidum DAL-1, complete genome  (1.1 MB, 1.1 million bp)
 - output: job_0000000204.txt (running time: about 40 min.)

Archaeal genome:

 - input: Archaeoglobus profundus DSM 5631, complete genome (1.5 MB, 1.5 million bp)
 - output: job_0000000205.txt (running time: about 20 min.)

Metagenomic sequence:

 - input: Human Genome Project - Buccal mucosa sample (SRS050007) (0.7 MB, 0.7 million bp)
 - output: job_0000000206.txt (running time: about 30 min.)
 - visualization of the output file: phylum composition of the buccal mucosa metagenome

Evaluation of the outputs:

- In the output file of the Treponema pallidum genome are only Treponema Pallidum assignments.
- In the output file of the Archaeoglobus profundus genome are only Archaeoglobus profundus assignments.
- The figure of the buccal mucosa metagenome shows a similar result as a diagram of the Human Microbiome Project (see Figure 2 in this article).


(Updated: Szept 8, 2014)