eCGF
What does it do?
The eCGF automator performs in silico CGF subtyping of Campylobacter using whole-genome sequence data in FASTA format
Check out the source code: github
How do I use it?
Subject
In the Subject field, put eCGF. Spelling counts, but case sensitivity does not.
Description
All you need to put in the description is a list of SEQIDs you want to process, one per line.
Example
For an example eCGF analysis, see issue 16196.
Interpreting Results
ECTyper will output a summary report, ISSUE_NUMBER_summary_report.csv that should look something like
the following excerpt:
| Genes | 11168_cj0008 | 11168_cj0033 | 11168_cj0035 | ... | Nearest Match | Number of Similarities (/40) | ... |
|---|---|---|---|---|---|---|---|
| 2018-LET-0106 | 0 | 0 | 1 | ... | 27_3_4 | 40 | ... |
| 2018-LET-0012 | 0 | 0 | 1 | ... | 926_2_1 | 40 | ... |
How long does it take?
eCGF is pretty fast - expect it to take a few seconds per genome you give it.
What can go wrong?
- Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.
- ?