VELVETOPTIMISER(1)

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 simultaneous 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.