Entering edit mode
7.8 years ago
Ric
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430
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
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.
Did you remove duplicates and trimming before you used SPAdes with the option "--trusted-contigs"?
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).
P.S. The reference assembly is smaller (1.3Gb) and the to assemble genome is bigger (3.3 Gb).