Alignment of mutli-contig fasta files

Question

[L Ron Hubbard]

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?

[GenoMax]

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?

[L Ron Hubbard]

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

Answer 1

[vmicrobio]

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

[L Ron Hubbard]

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

[vmicrobio]

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