Question: Alignment of mutli-contig fasta files
1
gravatar for L Ron Hubbard
3.4 years ago by
Cardiff
L Ron Hubbard10 wrote:

Hi,

I'm new to this so apologies if this question has been answered elsewhere:

I've recently sequenced 70 similar bacterial isolates using a MiSeq and assembled them using Spades. Each resulting fasta file has about 500 contigs.

My aim is to make each of these files into a single contig/scaffold, so that I can align with MUSCLE and then use FASTTREE to build the phylogeny.

Is there any way to do this?

alignment next-gen assembly • 1.4k views
ADD COMMENTlink modified 3.4 years ago by vmicrobio250 • written 3.4 years ago by L Ron Hubbard10

My aim is to make each of these files into a single contig/scaffold

If SPAdes was not able to create a single contig perhaps your sequence data is not complete. How can you fill-in data that is missing? Are you hoping to borrow from across samples i.e. essentially make single hybrid assembly?

ADD REPLYlink written 3.4 years ago by genomax91k

With bacteria, assemblies virtually always have multiple contigs. I think due to repeat elements. Can anyone confirm this?

ADD REPLYlink written 3.4 years ago by L Ron Hubbard10
0
gravatar for vmicrobio
3.4 years ago by
vmicrobio250
vmicrobio250 wrote:

you can use scaffold builder (source forge or online) to map your contigs against a reference in order to get a scaffold

ADD COMMENTlink written 3.4 years ago by vmicrobio250

Hi Haro, I tried that but the scaffold still produces the same number of contigs. Any ideas?

ADD REPLYlink written 3.4 years ago by L Ron Hubbard10

Hi, you may try quast to evaluate the quality of the assembly. Maybe the coverage is not homogenous or there is a lot of repeated sequences which may affect the assembly

ADD REPLYlink written 3.4 years ago by vmicrobio250
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