Reference guided assembly of contigs

Question

[hman6.2.91]

Hi guys, I need your help, I have some *.fna files containing contigs from some bacterial samples (two different species). I have to find a way to assemble the genome of each specie using those contigs. the professor I'm working with also told me he doesn't want to use a de-novo approach so I have to put together those genomes using the current reference genome for both bacteria species. How can I do that? I already tried Aligngraph but It needs some read files I don't have. I absolutely need to find one or more tools to do that...

Answer 1

[Sej Modha]

I'd try IDBA-hybrid with --reference option or SPAdes with --trusted-contigs option.

[hman6.2.91]

Thanks, I'll try them.

Answer 2

[hman6.2.91]

It's me again (lol?!) I'm trying to use SPAdes since it's the tool installed on my lab's server however I'm having troubles with the manual, It tells me to use the "--only-assembler" option with the trusted contigs one but I cant find how to specify the reference genome for the Hybrid approach... Anyone who ever used it?

[Buffo]

spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly

[Sej Modha]

You are trying to look for a --reference option in SPAdes but it is an option specific to idba-hybrid.

[Buffo]

For a very close related species SPADES works even better and faster than IDBA_hybrid.

[hman6.2.91]

The problem is that THE PROFESSOR told me to go with a reference guided approach so I'm stuck with that :(

[Joe]

Just install SOAP/Velvet/MIRA or any other number of assemblers that have a reference guided option. You can often install (well written) software in your local or home directory on a server.