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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-28 14:07:31 -05:00
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QuickStart-EukPhylo.md

@ -50,14 +50,15 @@ EukPhylo part 1 runs CDS (genome) or assembled transcripts (transcriptome) throu
```
python wrapper.py -1 1 -2 7 --assembled_transcripts AssembledTranscripts -o Output_Folder --genetic_code Universal -d Databases > log.txt
```
Code flags:
* -1 = start/first script to run.
* -2 = end/last script to run.
* --assembled_transcripts = path to folder with Assembled transcripts in fasta format.
* -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.
| Parameter | Description|
| ----------- |----------------- |
| -1 | start/first script to run.|
| -2 | end/last script to run.|
| --assembled_transcripts | path to folder with Assembled transcripts in fasta format.|
| -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.|
### Output:
> ReadyToGo files = AA, NTD