what are the best metagenome assemblers?

Question

[Rubemsilva32]

I am starting in the field of bioinformatics, could you indicate good metagenome assemblers?

[h.mon]

Please read:

(short version) - [[ Please read before posting a question ::: How To Ask A Good Question ]]

(long version) - How To Ask Good Questions On Technical And Scientific Forums

Then edit your post to include more information, such as the what type of data you have, how much data, and so on. Also, perform a good bibliographic review and see which assemblers would do a good job for your data.

Answer 1

[Mensur Dlakic]

Don't know how one can choose the best assembler, but these two should be a good starting point:

• https://github.com/voutcn/megahit
• http://cab.spbu.ru/software/spades/

Answer 2

[juanjo75es]

Actually, if you are dealing with viruses or phages these are the best assemblers compared using a public benchmark set:

s-aligner is first followed by metaSPAdes.

Reference: s-aligner: a greedy algorithm for non-greedy de novo genome assembly

Answer 3

[956120746]

Hi: After the test in our lab, mitofinder --metaspades gain the best result, you can also get mitochondrial data.

[juanjo75es]

Is there any difference between mitofinder -metaspades and just metaSPAdes? Looks like mitofinder is not an assembler and just calls metaSPAdes.