Table 1 Summary of barcrawl command-line options.
Option | Default | Min1 | Max2 | Effect |
|---|---|---|---|---|
-l <int> | = 8 | 1 | 20 | Set length of barcodes |
-m <int> | >= 3 | 1 | barcode length | Minimum base substitutions between barcode pairs |
-p <int> | >= 3 | 2 | N | Exclude homopolymers of specified length or greater |
-a <int> | >= 5 | 2 | N | Exclude hairpins of specified length or greater |
-b <int> | >= 5 | 2 | N | Exclude heteroduplexes of specified length or greater |
-f5 <string> | - | - | - | Specify 5' addition to barcode sequence |
-f3 <string> | - | - | - | Specify 3' addition to barcode sequence |
-j5 | off | - | - | Exclude barcodes with 5' base same as 3' end of upstream primer |
-j3 | off | - | - | Exclude barcodes with 3' base same as 5' end of downstream primer |
-r <string> | - | - | - | Specify reverse primer sequence |
-g <int> | > 70 | 50 | 100 | Exclude barcodes with % GC content greater than value |
-c <int> | < 30 | 0 | 50 | Exclude barcodes with % GC content less than value |
-d | on | - | - | Exclude barcodes that are converted to other barcodes by deletion |
-w | off | - | - | Order output by number of 454 GS-FLX nucleotide flows |
-o <string> | out.txt | - | - | Specify output file |
-v | off | - | - | Set verbose output to terminal |
-h | off | - | - | Display help |