Reference guided assembly methods
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5.4 years ago
Ric ▴ 370

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 • 5.8k views
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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.

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

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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).

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

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5.4 years ago
Sej Modha 5.0k

You could use idba-hybrid for reference guided assembly.

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