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lecture_notes:04-26-2010

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lecture_notes:04-26-2010 [2010/04/28 13:19]
galt
lecture_notes:04-26-2010 [2010/04/28 13:56] (current)
galt
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     * Can change the max-kmer maximum size at compilation     * Can change the max-kmer maximum size at compilation
       * 31mers are max size for a 64-bit word       * 31mers are max size for a 64-bit word
-    * Can add solid support by adding in a "de" tag for double-encoded +    * Can add solid support by adding in a "_de" tag for double-encoded. 
-    * Velvet is one of the only tools supporting colorspace reads+    * Velvet is one of the only de-novo assembly ​tools supporting colorspace reads
   * ~velvet/​data   * ~velvet/​data
     * Contains a simulated genome with simulated reads which can be used for testing the data     * Contains a simulated genome with simulated reads which can be used for testing the data
-    * No documentation ​which describes the files within this diretory+    * No documentation describes the files within this directory
   * ~velvet/​contrib -- Contributors directory   * ~velvet/​contrib -- Contributors directory
-    * estimate-exp_cov ​-- Estimates expected coverage+    * velvet-estimate-coverage.pl ​-- Estimates expected coverage
       * Maybe reading the stats.txt file which velvet produces       * Maybe reading the stats.txt file which velvet produces
     * VelvetOptimiser-2.1.0     * VelvetOptimiser-2.1.0
       * Written to try to find the best parameters for assembling the genome       * Written to try to find the best parameters for assembling the genome
 +      * Did not work, got stuck on local maximum for exp_cov and cov_cutoff
   * ~assemblies/​Pog/​velvet-assembly1   * ~assemblies/​Pog/​velvet-assembly1
     * Run velvet without any arguments under the assumption that velvet with estimate some correct parameters     * Run velvet without any arguments under the assumption that velvet with estimate some correct parameters
     * README ​     * README ​
-    * Ran without using any quality values. +    * Ran without using any quality values. ​ ​Velvet does not use quality values ​even if using fastq input files.
-      * May take quality values ​from .qual values+
     * Runs in 5-8 minutes     * Runs in 5-8 minutes
     * First estimated coverage and cutoff values were terrible. ​     * First estimated coverage and cutoff values were terrible. ​
lecture_notes/04-26-2010.1272485963.txt.gz · Last modified: 2010/04/28 13:19 by galt