Amos2ace

Overview

Amos2ace can be used to convert assembler output in the AMOS message format to the .ACE format (readable by consed).

Synopsis

amos2ace [options] <infile1> <infile2> ...

Amos2ace reads one or more AMOS message files specified on the command line and produces a .ACE file. The message files must be provided in a "reasonable" order: the file defining a specific object must occur before a file using it. The output file name is generated from the first file on the command line unless specifically set through option -o (see below).

Options

• -o <outfile> - place output in <outfile>
• -c <chromat_dir> - the chromatograms can be found in directory <chromat_dir>
• -p <phd_dir> - the PHD files can be found in directory <phd_dir>

Note: the chromat_dir and phd_dir parameters are only used to provide consed with the necessary information used to display chromatograms. These options are only relevant if the assembler inputs were generated using the phred pipeline.