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Updated PhyloToL Part 1: GF assignment (markdown)

Auden Cote-L'Heureux 2025-01-10 10:54:10 -05:00
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PhyloToL-Part-1:-GF-assignment.md

@ -103,7 +103,7 @@ Other available parameters are:
| --assembled_transcripts |string|Path to a folder of assembled transcripts, assembled by rnaSPAdes. | Each assembled transcript file name should start with a unique 10 digit code, and end in "_assembledTranscripts.fasta", E.g. Op_me_hsap_assembledTranscripts.fasta |
| --databases| string| Path to databases folder | The folder should contain all 3 databases|
| --output|string|Path for the output files | An "Output" folder will be created at this directory to contain all output files. By default this folder will be created at the parent directory of the Scripts folder |
|--xplate_contam |flag (true/false) | include or exclude | Run cross-plate contamination removal (includes all files) |
|--xplate_contam |flag (true/false) | include or exclude the argument | Run cross-plate contamination removal (includes all files) |
| --genetic_code |string|A .txt or .tsv with two tab-separated columns, the first with the ten-digit codes and the second column with the corresponding genetics codes| If all of your taxa use the same genetic code, you may enter it here. Alternatively, if you need to use a variety of genetic codes but know which codes to use, you may fill give here the path to a file. |
|--conspecific_names |string| A .txt or .tsv file with two tab-separated columns; the first should have 10 digit codes, the second species or other identifying names|This is used to determine which sequences to remove (only between "species") in index switching (cross-plate contamination) assessment. |
| --minlen |integer| any positive integer| Minimum transcript length |