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annotate README @ 0:435711ba68e3 draft

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author drosofff
date Fri, 29 May 2015 12:41:13 -0400
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1 #Created 28/11/2014
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2 #Christophe Antoniewski, CNRS/University Pierre et Marie Curie, drosofff@gmail.com
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3 # inspired from the oases wrapper developped by Konrad Paszkiewicz, Exeter Sequencing Service, University of Exeter
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4
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5 Oases optimiser
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6
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7 This Galaxy tool is intended to provide a crude but effective method of producing semi-optimised transcriptome assemblies.
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8 It operates by performing a number of user defined Velvet assemblies upon which Oases is then run.
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9 The results of all of these runs are then put through a final Oases step where they act as scaffolds for the main assembly.
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10 Note that this wrapper is designed to focused on small RNA reads from small RNA sequencings and will run velvetg with kmers ranging from 11 to 35
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11 Prerequisites:
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12
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13 1. Enclosed scripts
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14 2. package_ged_velvet and package_ged_oases dependency packages
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15
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16 Limitations:
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17
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18 This is a crude optimisation step which DOES NOT try to evaluate the quality of each assembly or map to any reference cDNA.