Galt's lecture on velvet
  * A lot of parameters with velvet to work with
  * Easy to install compared to other tools like allpaths
  * /campus/BME235/programs/velvet/ is the home directory
    * To install, simply type 'make'
    * Copy binaries
    * Can change the max-kmer maximum size at compilation
      * 31mers are max size for a 64-bit word
    * Can add solid support by adding in a "_de" tag for double-encoded.
    * Velvet is one of the only de-novo assembly tools supporting colorspace reads
  * ~velvet/data
    * Contains a simulated genome with simulated reads which can be used for testing the data
    * No documentation describes the files within this directory
  * ~velvet/contrib -- Contributors directory
    * velvet-estimate-coverage.pl -- Estimates expected coverage
      * Maybe reading the stats.txt file which velvet produces
    * VelvetOptimiser-2.1.0
      * 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
    * Run velvet without any arguments under the assumption that velvet with estimate some correct parameters
    * README 
    * Ran without using any quality values.  Velvet does not use quality values even if using fastq input files.
    * Runs in 5-8 minutes
    * First estimated coverage and cutoff values were terrible. 
    * Largest contig 713 bp long with an n50 of 27.
    * Assembling a single lane did better with only 1 lane, rather than two gave much better results
  * ~assemblies/test/velvet-assembly2
    * Running velvet on simulated 100kb genome with 35bp and 100bp reads.
    * Lowering the kmer value to 21 yielded a genome of 99975/100000 bases
    * Read length and error rate combined with longer kmer lengths may cause problems.
      * A single error in a read may prevent overlapping of K-mers.
      * A kmer is too long then you may not get overlapping
      * A kmer is too short, then you get too much overlapping where it shouldn't occur
    * Starting running on hgw-dev in order to get help from Daniel Zerbino
      * Used less options: -short
      * estimated coverage cutoff 13 which was right
      * saw some larger contigs: 21211max and 5554 n50
      * ran both short and long reads from the same 454 data.
        * Documentation states that short and long reads are the same except for sme tracking data which is potentially expensive
        * 82889max, 28393 n50
      * Combining both lanes of the 454 yielded 142283 max and 50864 n50.
  *~assemblies/Pog/velvet-assembly? 
    * Using flowspace data collapsed some nodes
    * -long_multi_cutoff 4 (over default 2)
      * Have to have seen it multiple times before you 
      * Showed improvements around 8 multi_cutoff
      * Lowering cov_cutoff
        * max 680241, 224364 n50
        * This is the best so far
    * large kmer values don't show too much of an improvement
  * velvet-assembly2
    * utilizes -shortPaired reads
    * Can also utilize unpaired reads as -short
    * may have some problems with reversing f3 primer
    * insert length 2200 (estimated by mapping paired reads onto 454 contigs from newbler)
    * adjusting other paramets did not improve assembly
    * Combining short and long data did not seem to help

Evaluating assembled genomes
  * contig-lengths.rdb within assembly directories
  * 
    * bottom of bin \t number of bin \t 
  * take contigs and use various search tools, megablast, blastn, blat-strict-match, differences, differences.short
    * megablast fast but numb (not sensitive)
    * blastn sensitive
    * blat very sensitive. produces psl output.
      * psl longs can get very long
      * labeled table at the top
      * Filter program blat-strict-match selects the best matches.
    * Differences
      * shows differences between assemblies on the pieces that can map
      *