Question: Reference guided assembly methods
2
gravatar for Ric
4.4 years ago by
Ric330
Australia
Ric330 wrote:

Hello, I am interested in reference-guided assembly and found this paper ( http://www.pnas.org/content/108/25/10249.full ). Is this still the best way to do a reference-guided assembly or are there any better papers available how to do it and which provide maybe some command examples?

Thank you in advance.

Mic

assembly • 4.9k views
ADD COMMENTlink modified 4.4 years ago by Sej Modha4.7k • written 4.4 years ago by Ric330
1

I've been told MIRA is a decent assembler for reference guided purposes (though never used it myself and have been told that the manual is a nightmare).

SPAdes also has the option of providing trusted contigs which I've used in the past for assembling plasmids.

ADD REPLYlink written 4.4 years ago by Joe18k

Did you remove duplicates and trimming before you used SPAdes with the option "--trusted-contigs"?

ADD REPLYlink written 4.4 years ago by Ric330

Reads were already trimmed, but I didn't remove any duplicates. Managed to get a single contig out without the need to downsample reads as well (MiSeq of plasmid gave avg 2000X coverage).

ADD REPLYlink written 4.4 years ago by Joe18k

P.S. The reference assembly is smaller (1.3Gb) and the to assemble genome is bigger (3.3 Gb).

ADD REPLYlink written 4.4 years ago by Ric330
4
gravatar for Sej Modha
4.4 years ago by
Sej Modha4.7k
Glasgow, UK
Sej Modha4.7k wrote:

You could use idba-hybrid for reference guided assembly.

ADD COMMENTlink written 4.4 years ago by Sej Modha4.7k
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: 1959 users visited in the last hour