Question: How to create scaffolds from contigs?
0
gravatar for agata88
2.3 years ago by
agata88790
Poland
agata88790 wrote:

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

de novo • 1.8k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by agata88790
1

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.

ADD REPLYlink written 2.3 years ago by Buffo1.6k

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?

ADD REPLYlink written 2.3 years ago by agata88790

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.

ADD REPLYlink written 2.3 years ago by Buffo1.6k

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

ADD REPLYlink written 2.3 years ago by Buffo1.6k

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by agata88790

You can extract consensus sequence automatically from IGV.

ADD REPLYlink written 2.3 years ago by Buffo1.6k

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

ADD REPLYlink written 2.3 years ago by agata88790
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1603 users visited in the last hour