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.

velvetoptimiser 2.2.5                               June 2014                                 VELVETOPTIMISER(1)