Option | Default | Min | Max | Effect |
---|---|---|---|---|
-in <string> | - | - | - | Fasta sequence file to process |
-qin <string> | <fasta_file_name.qual> | - | - | Quality scores associated with sequences |
-map <string> | <fasta_file_name.bar> | - | - | Tab delimited file listing barcodes and associated metadata |
-out <string> | <fasta_file_name> | - | - | Base name for output files |
-for <string> | - | - | - | Forward primer sequence |
-rev <string> | - | - | - | Reverse primer sequence |
-rnm <string> | off | - | - | Toggle on renaming of sequences based on column of barcode file named by specified string |
-spl <string> | off | - | - | Toggle on splitting sequences into individual files based on column of barcode file named by specified string |
-rep | off | - | - | Toggle on dereplication of output sequence file(s) |
-st <int> | 1 | 1 | N | Position of barcode in sequence |
-qu <int> | 20 | 0 | N | Minimum acceptable quality score, averaged over window |
-win <int> | 5 | 1 | N | Window for calculation of mean quality score |
-min <int> | 200 | 1 | N | Minimum acceptable sequence length |
-amb <int> | 0 | 0 | N | Maximum acceptable number of ambiguous bases |
-xbar | - | - | - | Toggle off removal of barcodes from sequences |
-v | off | - | - | Verbose output to stdout |
-dry | off | - | - | Dry run - report sequence statistics then quit |
-h | off | - | - | Display help |