This is the command velvetoptimiser that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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.
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