diff --git a/PhyloToL-Part-1:-GF-assignment.md b/PhyloToL-Part-1:-GF-assignment.md index 273242f..f44356d 100644 --- a/PhyloToL-Part-1:-GF-assignment.md +++ b/PhyloToL-Part-1:-GF-assignment.md @@ -87,7 +87,7 @@ Available parameters are: | --output|str|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 |-|- | Run cross-plate contamination removal (includes all files) | | --genetic_code |str|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 |str| 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 cross-plate contamination assessment. | +|--conspecific_names |str| 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 |int| -| Minimum transcript length | | --maxlen |int|-| Maximum transcript length | | --seq_count |int|-| minimum number of sequences after assigning OGs |