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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.