NAME

       velvetoptimiser - Automatically optimise Velvet do novo assembly parameters

SYNOPSIS

       velvetoptimiser [options] -f 'velveth input line'

DESCRIPTION

       VelvetOptimiser  is  a  multi-threaded  Perl script for automatically optimising the three
       primary parameter options (K, -exp_cov, -cov_cutoff)  for  the  Velvet  de  novo  sequence
       assembler.

OPTIONS

       --help This help.

       --version!
              Print version to stdout and exit. (default '0').

       --v|verbose+
              Verbose logging, includes all velvet output in the logfile. (default '0').

       --s|hashs=i
              The starting (lower) hash value (default '19').

       --e|hashe=i
              The end (higher) hash value (default '31').

       --x|step=i
              The step in hash search..  min 2, no odd numbers (default '2').

       --f|velvethfiles=s The file section of the velveth command line. (default '0').

       --a|amosfile!
              Turn on velvet's read tracking and amos file output. (default '0').

       --o|velvetgoptions=s Extra velvetg options to pass through.
              eg. -long_mult_cutoff -max_coverage etc (default '').

       --t|threads=i
              The maximum number of simulataneous velvet instances to run. (default '4').

       --g|genomesize=f The approximate size of the genome to be assembled in megabases.
              Only  used  in  memory use estimation. If not specified, memory use estimation will
              not occur. If memory use is estimated, the  results  are  shown  and  then  program
              exits. (default '0').

       --k|optFuncKmer=s The optimisation function used for k-mer choice. (default 'n50').

       --c|optFuncCov=s  The  optimisation  function  used  for cov_cutoff optimisation. (default
              'Lbp').

       --m|minCovCutoff=f The minimum cov_cutoff to be used. (default '0').

       --p|prefix=s
              The prefix for the output filenames, the default is the date and time in the format
              DD-MM-YYYY-HH-MM_. (default 'auto').

       --d|dir_final=s The name of the directory to put the final output into. (default '.').

       --z|upperCovCutoff=f  The  maximum  coverage  cutoff  to  consider  as a multiplier of the
              expected coverage. (default '0.8').

       Advanced!: Changing the optimisation function(s)

       Velvet optimiser assembly optimisation function can be built from the following variables.

              LNbp = The total number of Ns in large contigs Lbp = The total number of base pairs
              in large contigs Lcon = The number of large contigs max = The length of the longest
              contig n50 = The n50 ncon = The total number of contigs tbp = The total  number  of
              basepairs in contigs

   Examples are:
              'Lbp'  =  Just  the total basepairs in contigs longer than 1kb 'n50*Lcon' = The n50
              times the number of long contigs.  'n50*Lcon/tbp+log(Lbp)'  =  The  n50  times  the
              number of long contigs divided

              by  the  total  bases  in  all  contigs plus the log of the number of bases in long
              contigs.