Velvet Assembly Parameters

Question

[']

I am completely new to Velvet, and I am mainly using "Vague" GUI to work with Velvet. I have been trying to experiment a lot with all the parameters, but now I wish to understand which parameters mainly are best suited for my dataset.

I have two .fq files, one being the first mates on the forward strand, and the other being the second mates on the reverse strand. Average length of both is 70bp. Outer distance between two pairs is around 500bp. I want to assembly the genomes and get the reference.

I wish to know if I am in the right track at all. What I am doing is that I am choosing a k-mer size of 31. Coverage cutoff and expected coverage and Minimum contig length are all set to Auto. Read type: paired end. Interleaved sequence file: separate.

The full task is here:

What does "assemble the other genome" refer to? The task in general is quite unclear to me.

[h.mon]

Do you have to use Velvet? There are probably better tools for this task than Velvet. This is homework, so I don't want to give out too much, but you will probably assemble a good draft for one bacteria and not the other, but as they are related you may use the draft to guide the assembly of the second strain.

As a side note, the first sequence of the question is really confusing.

[']

Thank you for your answer. No, I do not have to use Velvet. Basically this is just a voluntary project work to get familiar with genome assembly, and since nobody will check it then it does not matter what tool I use.

[christopher medway]

Have you looked at velvetoptimiser?

[Rayan Chikhi]

h.mon's comment should be the answer to this post

Answer 1

[elbecerrasoto]

For the novo assembly use the assembler spades for illumina mate pairs is as easy as to type this in the linux termial:

spades.py --mp1-1 /home/user/path/to/first.fq --mp1-2 /home/user/path/to/second.fq -o /home/user/path/to/output/

More information about it and the installation guide are in the the following link: http://bioinf.spbau.ru/spades

Spades is easy to use because the software tries several k-mer lengths and choose the best one, also the default parameters are generally the good ones so you don't need to worry about that.

Answer 2

[Antonio R. Franco]

What organism is the DNA coming from? If it has a reference genome, you can order contigs and evaluate the right kmer using Mauve. Kmer chosen will produce a deep change in the quality of the assembly There are some tutorials published that can be found googleling