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Reference guided assembly of contigs

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...

assembly bacteria contigs
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updated by Ram Ram • written by hman6.2.91 • hman6.2.91

2 answers

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

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written by Sej Modha Sej Modha

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?

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written by hman6.2.91 • hman6.2.91 
spades.py --only-assembler --trusted-contigs trusted_contigs.fa -1 file_r1.fastq -2 file_r2.fastq -o spades_hybrid_assembly
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written by Buffo Buffo

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

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written by Sej Modha Sej Modha

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

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written by Buffo Buffo

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

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written by hman6.2.91 • hman6.2.91

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.

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written by Joe Joe

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