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commit ca7790da3aaef1dbab3bc0e430f47004f1b8699f Author: Andreas Tille <ti...@debian.org> Date: Mon Jun 30 11:02:03 2014 +0000 Add help2man based manpage --- debian/manpages | 1 + debian/velvetoptimiser.1 | 77 ++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 78 insertions(+) diff --git a/debian/manpages b/debian/manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/manpages @@ -0,0 +1 @@ +debian/*.1 diff --git a/debian/velvetoptimiser.1 b/debian/velvetoptimiser.1 new file mode 100644 index 0000000..53be6a5 --- /dev/null +++ b/debian/velvetoptimiser.1 @@ -0,0 +1,77 @@ +.TH VELVETOPTIMISER "1" "June 2014" "velvetoptimiser 2.2.5" "User Commands" +.SH NAME +velvetoptimiser \- Automatically optimise Velvet do novo assembly parameters +.SH SYNOPSIS +.B velvetoptimiser +[\fI\,options\/\fR] \fI\,-f 'velveth input line'\/\fR +.SH 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. +.SH OPTIONS +.TP +\fB\-\-help\fR +This help. +.TP +\fB\-\-version\fR! +Print version to stdout and exit. (default '0'). +.TP +\fB\-\-v\fR|verbose+ +Verbose logging, includes all velvet output in the logfile. (default '0'). +.TP +\fB\-\-s\fR|hashs=i +The starting (lower) hash value (default '19'). +.TP +\fB\-\-e\fR|hashe=i +The end (higher) hash value (default '31'). +.TP +\fB\-\-x\fR|step=i +The step in hash search.. min 2, no odd numbers (default '2'). +.HP +\fB\-\-f\fR|velvethfiles=s The file section of the velveth command line. (default '0'). +.TP +\fB\-\-a\fR|amosfile! +Turn on velvet's read tracking and amos file output. (default '0'). +.TP +\fB\-\-o\fR|velvetgoptions=s Extra velvetg options to pass through. +eg. \fB\-long_mult_cutoff\fR \fB\-max_coverage\fR etc (default ''). +.TP +\fB\-\-t\fR|threads=i +The maximum number of simulataneous velvet instances to run. (default '4'). +.TP +\fB\-\-g\fR|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'). +.HP +\fB\-\-k\fR|optFuncKmer=s The optimisation function used for k\-mer choice. (default 'n50'). +.HP +\fB\-\-c\fR|optFuncCov=s The optimisation function used for cov_cutoff optimisation. (default 'Lbp'). +.HP +\fB\-\-m\fR|minCovCutoff=f The minimum cov_cutoff to be used. (default '0'). +.TP +\fB\-\-p\fR|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'). +.HP +\fB\-\-d\fR|dir_final=s The name of the directory to put the final output into. (default '.'). +.HP +\fB\-\-z\fR|upperCovCutoff=f The maximum coverage cutoff to consider as a multiplier of the expected coverage. (default '0.8'). +.PP +Advanced!: Changing the optimisation function(s) +.PP +Velvet optimiser assembly optimisation function can be built from the following variables. +.IP +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 +.SS "Examples are:" +.IP +\&'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 +.IP +by the total bases in all contigs plus the log of the number of bases +in long contigs. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/velvetoptimiser.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit