Reference guided assembly of contigs
2
0
Entering edit mode
4.5 years ago
hman6.2.91 • 0

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...

contigs bacteria Assembly reference tools • 5.2k views
ADD COMMENT
2
Entering edit mode
4.5 years ago
Sej Modha 5.0k

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

ADD COMMENT
0
Entering edit mode

Thanks, I'll try them.

ADD REPLY
0
Entering edit mode
4.5 years ago
hman6.2.91 • 0

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 COMMENT
0
Entering edit mode
spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly
ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1801 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6