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Updated QuickStart EukPhylo (markdown)

Godwin Ani 2025-01-27 15:01:43 -05:00
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QuickStart-EukPhylo.md

@ -54,13 +54,13 @@ Here add detail of each option possible:
* -2 = end script * -2 = end script
* --assembled_transcripts = Folder with Assembled transcripts in fasta format * --assembled_transcripts = Folder with Assembled transcripts in fasta format
* -o = path to output folder * -o = path to output folder
* --genetic_code = specified genetic code, name of .txt file with Genetic codes * --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional
* -d = path to Databases folder * -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
### Output: ### Output:
* ReadyToGo = AA, NTD * ReadyToGo = AA, NTD
* Sequences summary * Sequences statistics and summary
### Modularity of options and replacing the Hook database ### Modularity of options and replacing the Hook database
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. 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.
@ -87,13 +87,13 @@ Here add detail of each options possible:
* -2 = end script * -2 = end script
* --cds = Folder with CDS files in fasta format * --cds = Folder with CDS files in fasta format
* -o = path to output folder * -o = path to output folder
* --genetic_code = specified genetic code, name of .txt file with Genetic codes * --genetic_code = specified genetic code, name of .txt file with Genetic codes; optional
* -d = path to Databases folder * -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
### Output: ### Output:
* ReadyToGo = AA, NTD * ReadyToGo = AA, NTD
* Sequences summary * Sequences statistics and summary
### Modularity of options and replacing the Hook database ### Modularity of options and replacing the Hook database
EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options. EukPhylo part 1 for genomes is composed of 5 scripts. User can choose to start or stop at each step by changing the -1 and/or -2 options.