How to create scaffolds from contigs?

Question

[agata88]

Hi all!

I was using velveth and velvetg to create contigs.fa file. It includes all sequences with kmer=31, min contig length 100 and expected coverage 5.

Now I would like to create scaffolds, which tool do you recommend for this purpose?

Thanks in advance,

Best,

Agata

[Buffo]

Spades and IDBA (which I know) but why don´t you play with kmer lenght? With that programs you can make assembly using different kmer lenghts.

*That programs makes scaffolds after contigs assembly but using read`s information.

[agata88]

Thanks but velvet does not support higher kmer length than 31. I see that Spades and IDBA need fastq files as input not contig file. Do you know any tool that can concatenate contings into scaffolds with the use of contig fasta file?

[Buffo]

Sorry I dont know, Reads are used to infer distance between contigs and then make scaffolds, so If you dont have them, it is complicated issue, but; If you have a reference genome (or genome from related specie) you can map to it these contigs ( with Bowtie2 or BWA) and then make scaffolds ussing coordinates if it is posible after mapping.

[Buffo]

Even you can extract consensus sequence from IGV after mapping contigs to reference genome.

[agata88]

Thanks I'll try that, although I would like to do it as much automatic as possible :) extracting manually consensus sequence is not comfortable in this case.

[Buffo]

You can extract consensus sequence automatically from IGV.

[agata88]

Thanks, SPADES is doing really good job :) I used fastq raw files and quit velvet. Best, Agata