VELVETOPTIMISER(1)

💖 VELVETOPTIMISER 💖

okay bestie, so this is the manual page for velvetoptimiser — a User Commands situation, and literally the whole point is that it auto-optimises your Velvet de novo assembly parameters. No cap. Let me walk you through it 🫶

✨ NAME ✨

velvetoptimiser — Automatically optimise Velvet do novo assembly parameters

(yes bestie it says "do novo" in the original and I am NOT fixing it, that's canon now, we respect the source 💅)

🌸 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.

so basically: you hand it the messy stuff, it goes feral on the parameter space, and it finds you the slay config. multi-threaded too, so she's doing all that at once. main character energy fr fr 🔥

👑 OPTIONS 👑

• --help — This help. the classic. she's here for you 💖
• --version! — Print version to stdout and exit. (default '0').
• --v|verbose+ — Verbose logging, includes all velvet output in the logfile. (default '0'). turn this on if you want EVERYTHING, the whole tea ☕
• --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'). fr, min 2 and NO odd numbers, she's picky like that 🙈
• --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 ''). pass-through queen 👑
• --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').

heads up bestie: if you DO give a genome size, it estimates memory, prints the results, and then just... dips. program exits. it's not assembling anything, it's just doing a vibe check on your RAM 💀

• --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) 🌈

okay this is the part where it gets ~fancy~ ✨

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.

ngl that last one is giving math class but she's EATING, iykyk 💅 do not ask me to simplify it, that IS the expression, character for character, we do not touch the formula 🫶

and that's the whole page bestie!! this little love letter is from velvetoptimiser 2.2.5, dated June 2014, filed under User Commands as VELVETOPTIMISER(1) — old but iconic, and honestly? still slaying ⭐🌸💖

now go assemble something gorgeous, mwah 🧚‍♀️