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Table 2 Summary of bartab command-line options.

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

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