Question: Reference guided assembly of contigs
0
gravatar for hman6.2.91
2.9 years ago by
hman6.2.910
hman6.2.910 wrote:

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...

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by hman6.2.910
2
gravatar for Sej Modha
2.9 years ago by
Sej Modha4.6k
Glasgow, UK
Sej Modha4.6k wrote:

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

ADD COMMENTlink written 2.9 years ago by Sej Modha4.6k

Thanks, I'll try them.

ADD REPLYlink written 2.9 years ago by hman6.2.910
0
gravatar for hman6.2.91
2.9 years ago by
hman6.2.910
hman6.2.910 wrote:

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?

ADD COMMENTlink written 2.9 years ago by hman6.2.910
spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly
ADD REPLYlink written 2.9 years ago by Buffo1.8k

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

ADD REPLYlink written 2.9 years ago by Sej Modha4.6k

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

ADD REPLYlink written 2.9 years ago by Buffo1.8k

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

ADD REPLYlink written 2.9 years ago by hman6.2.910

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.

ADD REPLYlink written 2.9 years ago by Joe16k
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: 1111 users visited in the last hour