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Updated QuickStart EukPhylo (markdown)

Adri K. Grow 2025-02-04 10:12:26 -05:00
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QuickStart-EukPhylo.md

@ -60,7 +60,8 @@ Code parameters:
|`-o` | Path to output folder.|
|`--genetic_code` | Specified genetic code, name of .txt file with Genetic codes; optional.|
|`-d` | Path to Databases folder.|
|`> log.txt` | If added to the end of the command, it will output a log file with progress, warning, or error messages.|
|`> log.txt` | If added to the end of the command, it will output a log file with progress, warning, or error messages.|
|`-x`| Run cross-plate contamination (XPC). Only available for transcriptomes.|
### Output:
1. **ReadyToGo files = AA, NTD**
@ -70,8 +71,6 @@ Code parameters:
EukPhylo part 1 for transcriptomes is composed of 7 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.
If a user chooses to use their own gene family database, they need to replace the Hook.fasta file in the Databases folder and build a diamond version of their own file; with adjusting the naming system of sequences as the only requirement.
To add the XPC option, only available for transcriptomes, user need to add the -x option in their command line.
## Genomes:
### Set Up:
* A folder called “CDS” with your CDS fasta files