Can I Compile Velvet For K-Mer Of 201?

Question

[upendrakumar.devisetty]

I am trying to compile velvet to go a maximum k-mer length of "201" but velvet doesn't seem to respond to this. I am wondering is it possible to compile to that k-mer size?

Thanks Upendra

[upendrakumar.devisetty]

I will answer myself. Yes i can compile velvet to k-mer size of 201

[SES]

I just tried it and velvet compiled with the max k-mer length set to 201 just fine. You need to provide some more details, such as the exact command you tried and errors you see for us to help further.

By the way, I would rethink doing this (unless you have a good reason). It will use a lot of memory and your k-mer coverage will be low, so I suspect your assemblies will not be close to the length you expect with this setting.

[upendrakumar.devisetty]

Hi SES, Sorry this is the command that i used to compile velvet..... "make 'CATEGORIES=57' 'MAXKMERLENGTH=201' 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'OPENMP=1' 'BUNDLEDZLIB=1'" I don't need to worry about memory issues with this k-mer size since i have only 1million SE reads for a bacteria. The assembly finished within a couple of minutes. However as you say the assemblies weren't good with this k-mer size compared to lower k-mer size of 99.

[lexnederbragt]

I would rather use a different program, one that is based on Overlap Layout Consensus, e.g. Celera, MaSuRCA, MIRA (kind-of OLC),...

[upendrakumar.devisetty]

I first tried mira but it is giving me ~1300 contigs and so i though about using velvet. With velvet i am getting ~900 contigs with a higher N50 but unfortunately the overall size of assembly is smaller in velvet compared to mira. Hopefully i will stick with mira for now. What i next did was to reorder the contigs using MAUVE. I am wondering now to how to fill the gaps between these 1300 contigs to make them as big as possible. Any ideas?

[5heikki]

SSPACE is pretty handy for scaffolding..

[Rohit]

Spades works fine too. Why use Velvet for a bacterial assembly when you have less memory consuming tools. PCAP assembler works fine but keep in mind the quality filter.

[upendrakumar.devisetty]

Yeah you are true in that i could have tried other memory less intensive assemblers but since i have only 1million reads i decided to go ahead with it....

[Torst]

As a long time Velvet user for bacterial genomes, I would really suggest you try SPADES instead now.

http://thegenomefactory.blogspot.com.au/2013/08/how-spades-differs-from-velvet.html

Answer 1

[blanca]

upendrakumar.devisetty, how did you finally compile velvet with k-mer 201? I may be making the same mistake ...