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Table 1 Summary of barcrawl command-line options.

From: BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing

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
  1. 1Minimum value for numerical options.
  2. 2Maximum value for numerical options. N = any non-negative integer.