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toAmos: converter from various
types of inputs to AMOS messages
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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.
System requirements
toAmos is written in Perl. It requires Perl 5.6.0 or newer and was tested on several Unix systems including Linux RedHat 7.3, OSF5.1, Sun Solaris, and Linux SuSE 9.1 and should run on most systems UNIX systems.
Obtaining amos2ace
toAmos can be downloaded as a part of the AMOS package.
This software is OSI Certified Open Source
Software.
Documentation
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
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.
Contact Information
Please direct your questions and suggestions to:
