oasesoptimiser: README annotate

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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 17:09:27 -0400
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0 d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 #Created 07/01/2011
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 #Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 Oases optimiser
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 This Galaxy tool is intended to provide a crude but effective method of producing semi-optimised transcriptome assemblies. It operates by performing a number of user defined Velvet assemblies upon which Oases is then run. The results of all of these runs are then put through a final Oases step where they act as scaffolds for the main assembly.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 Prerequisites:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 1. Enclosed scripts
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 2. Working installation of Velvet and Oases
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 Limitations:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 This is a crude optimisation step which DOES NOT try to evaluate the quality of each assembly or map to any reference cDNA.