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We have some bacterial genomes that were assembled using Spades, they were sequenced with and IonTorrent PGM.

There are many assemblers and they give different results. I was interested in a tool that can merge the results from different assemblers but there are not many. I found only 2 : GARM and GAM-NGS.

Are there other tools to do merges? Does this improves the genome seq quality?

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  • $\begingroup$ I think, you might lose quality they have their own error system which is only partially considered. $\endgroup$
    – Devashish Das
    Commented Aug 13, 2014 at 4:18
  • $\begingroup$ do the different assemblers five very different results with similar parameters ? $\endgroup$
    – WYSIWYG
    Commented Aug 13, 2014 at 4:38

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This is an old question but it seems relevant to answer now given current state of art. See also this related thread on biostars.

There are now many tools that perform this function, which is somewhat routine. A partial list:

I don't know which is best. Quickmerge is the one that I remember seeing the most. I believe that it is more common with eukaryotic genomes than microbial, as microbial genomes are now often getting closed with long reads.

In general we should expect that the regions that are agreed-upon by the assemblers will be fairly trustworthy, e.g. "improved" potentially. Artifacts are more likely to be found by using this kind of comparison as well.

The strategies used in each case will depend upon which tool you use. I haven't used them enough to say for sure.

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