ToAmos

toAmos: converter from various types of inputs to AMOS messages

Overview

toAmos is primarily designed for converting the output of an assembly program into the AMOS format so that it can be stored in an AMOS bank. toAmos can be used as a replacement for tarchive2amos however the latter is more flexible when converting from Trace Archive or simple .seq and .qual inputs.

Synopsis

toAmos (-m mates|-x traceinfo.xml|-f frg)
       (-c contig|-a asm|-ta tasm|-ace ace|-s fasta|-q qual)
        -o outfile
       [-i insertfile | -map dstmap]
       [-gq goodqual] [-bq badqual]

toAmos reads the inputs specified on the command line and converts the information into AMOS message format. The following types of information can be provided to toAmos:

• Sequence and quality data (options -f, -s, -q, -gq, or -bq)
• Library and mate-pair data (options -m, -x, -f, -i, or -map)
• Contig data (options -c, -a, -ta, or -ace)
• Scaffold data (option -a)

Options

• -o <outfile> - place output in <outfile>
• -m <matefile> - library and mate-pair information in Bambus format
• -x <trace.xml> - ancilliary data (library, mate-pair, clear range) in Trace Archive format
• -f <frg file> - library, mate-pair, sequence, quality, and clear range data in Celera Assembler message format
• -s <fasta> - sequence information in multi-FASTA format
• -q <qual> - quality information in multi-FASTA format
• -gq <goodqual> - if no quality file provided bases within clear range are assigned this quality value (default 30)
• -bq <badqual> - if no quality file provided bases outside the clear range are assigned this quality value (default 10)
• -a <asm file> - contig and scaffold information in Celera Assembler message format
• -c <contig file> - contig information in TIGR Assembler GDE-like output
• -ta <TA asm file> - contig information in TIGR Assembler .asm output
• -ace <ace file> - contig information in ACE format
• -map <dstmap> - mapping from internal library ID to external library ID useful in conjunction with the -f option. This file consists of space-separated records providing a mapping from the "acc:" field in "DST" records within the .frg file to an externally recognizable name for each library.

TIGR specific options (not too useful outside TIGR)

• -i <insert file> - use mapping from internal library ID to external library ID provided in a .insert file produced by pullfrag.

Known issues

Notes

The -ta (TIGR Assembler input) and -ace (ACE formatted input) options have not been throughly tested and likely do not properly work. Contact us if either of these options is important to you.