Minia-genome assembler

[bioman1]

Hello,

I am working in the plant genome assembly. I am working on workstation, my fastq file (interleaved as single fastq file) is about 120Gb. I cannot able use velvet, soapdenovo due to memory constraint. I am trying to assemble with minia, which uses very low memory. Although, minina give comparable N50 to other frequently used genome assembler. I wonder why this assembler not used much in genome assembly project?. If I use this assembler, do I have any problem in publication?

[WhatsOEver]

You probably haven't seen the publication of the assembler, have you? (Space-efficient and exact de Bruijn graph representation based on a Bloom filter, http://www.almob.org/content/8/1/22)

Though the impact factor of ABM is quite low, it is peer-reviewed, so you shouldn't have any problems when using it.
The reason why it hasn't been cited much is probably that it is quite new?!

[rchikhi]

As an author, I also wonder why

You should have no problem submitting the results of a Minia assembly to a conference/journal. Actually, if anyone feels otherwise, please state your concern (the software is still actively supported by its authors).

[samanta]

The first rule of using Minia assembler: You do not talk about Minia assembler.

The second rule of using Minia assembler: You do not talk about Minia assembler.

Third rule of using Minia assembler: Someone yells stop, goes limp, taps out, the assembly is over.

Fourth rule: assemble only large genomes with Minia, take wimpy bacterial ones to Velvet.

Fifth rule: one assembly at a time, fellas.

Sixth rule: no 512GB servers, no digital normalization.

Seventh rule: Assembly will go on as long as they have to.

And the eighth and final rule: If this is your first time assembling large genomes, you have to use Minia assembler.

[zs_03]

Can anyone tell me how to install minia software?

[rchikhi]

If you run linux 64 bits, then the binary is available here: http://minia.genouest.org/
Sources can be compiled too from there, but it takes a bit more effort.