Minia-genome assembler

bioman1 · 07-22-2014, 08:50 PM

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 · 07-23-2014, 03:23 AM

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 · 07-24-2014, 11:15 AM

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 · 08-21-2014, 09:39 PM

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 · 12-16-2015, 02:33 AM

Can anyone tell me how to install minia software?

rchikhi · 12-17-2015, 05:48 AM

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.

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07-22-2014, 08:50 PM	#1
bioman1 Member Location: US Join Date: May 2012 Posts: 80	Minia-genome assembler 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?

07-24-2014, 11:15 AM	#3
rchikhi Member Location: France Join Date: Jan 2013 Posts: 13	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). Last edited by rchikhi; 07-24-2014 at 11:22 AM.

08-21-2014, 09:39 PM	#4
samanta Senior Member Location: Seattle Join Date: Feb 2010 Posts: 109	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. __________________ http://homolog.us

07-23-2014, 03:23 AM	#2
WhatsOEver Senior Member Location: Germany Join Date: Apr 2012 Posts: 215	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?!

12-16-2015, 02:33 AM	#5
zs_03 Junior Member Location: India Join Date: Dec 2015 Posts: 1	Can anyone tell me how to install minia software?

12-17-2015, 05:48 AM	#6
rchikhi Member Location: France Join Date: Jan 2013 Posts: 13	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.