ASGARD 1.0

ASGARD is a metabolic pathway reconstruction software, but also generates other types of biological sequence annotation (GO numbers, BLAST reports). ASGARD tool is intended to be run in UNIX-like systems, and supports SGE or PBS.

ASGARD and its documentation are released under the GNU GPL v.3 and GNU FDL v. 1.2 (please see doc/COPYING and doc/DOC_LICENSE for the licenses).

Although EMBOSS is also released under the GPL, the source code is not included with ASGARD since the included binaries were compiled without modification from the original. If you want the source code for splitter, please contact me, or obtain it directly from the EMBOSS distribution.

Please check the manual (doc/ASG_manual.pdf) in the /doc directory for details on installing and using ASGARD and accompanying utilities.

Options:

-v displays program version and exits;
-h displays this help message and exits;

This program can be run starting with either long DNA sequences or gene sized DNA or protein sequences.

-w use this option if you have small sequences to annotate - they will NOT be broken into smaller sequences for BLAST. (default: long sequences) - GFF file is not created, -g and -s are ignored;
-B do first BLAST against general DB only and stop (no metabolic reconstruction);
-q start from second step of pipeline (BLAST against general DB previously done);
-z do only last step of pipeline (second, "reverse" BLAST already done);

Mandatory:

-i FASTA file with the sequence(s) you want to annotate;
-p BLAST program to use, one of blastn, blastp, blastx, tblastn or tblastx (consult the BLAST documentation if you do not know which one to use);
-d BLAST database to use (generated by formatdb, see BLAST docs; for metabolic reconstructions, this database is ideally derived from SwissProt; for general BLAST only, any database will do);
* [Next two options not needed for -B mode]
-f File with FASTA sequences corresponding to the BLAST database;
-l Location of mapping files, needed for last step of reconstruction (-z);

Optional:

-e E-value to be used in BLAST searches (default: 1e-6);
-P do not submit jobs to scheduling software (PBS/SGE);
-j maximum number of hits to return in each BLAST search (10);
-m output format for BLAST results (only valid for -B, default: 8);
-s size to break the original sequence, if you are not using -w (500 bp);
-n number of nodes to use for BLAST, first iteration (10);
-a number of processors per node to use for each BLAST command (1);
-k keep intermediary files (BLAST databases and results), default is deleting them - they can take a lot of space.
-b any additional parameters you want to use for BLAST, this HAS TO be surrounded by quotes (double or single), like "-F F" or '-F F', for example, or the output will be wrong.

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