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Search: Posts Made By: rchikhi
Forum: Bioinformatics 12-17-2015, 05:48 AM
Replies: 5
Views: 2,054
Posted By rchikhi
If you run linux 64 bits, then the binary is...

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.
Forum: Bioinformatics 07-24-2014, 11:15 AM
Replies: 5
Views: 2,054
Posted By rchikhi
As an author, I also wonder why :) You...

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...
Forum: Bioinformatics 05-28-2014, 08:52 AM
Replies: 10
Views: 2,299
Posted By rchikhi
Ty for the details -- slow disk system is the...

Ty for the details -- slow disk system is the only reason why Minia can be slow, so this makes sense.
Forum: Bioinformatics 05-28-2014, 08:04 AM
Replies: 10
Views: 2,299
Posted By rchikhi
Thanks for your comment. There's a...

Thanks for your comment.

There's a difference between accuracy of contigs (misassembly, mismatches) and contiguity (how long the contigs are).

Yes it make sense to say that Minia doesn't always...
Forum: Bioinformatics 05-27-2014, 05:35 PM
Replies: 10
Views: 2,299
Posted By rchikhi
Minia dev here. I regret to hear that for some of...

Minia dev here. I regret to hear that for some of you Minia has been inaccurate or too slow.

Minia is IO-intensive, so it can be slow if you run it on a network-mounted folder (e.g. your...
Forum: Bioinformatics 03-21-2014, 06:28 AM
Replies: 2
Views: 992
Posted By rchikhi
Here is a mirror: ...

Here is a mirror:

http://bx.psu.edu/~rxc48/minia-1.6333.tar.gz

and for DSK:

http://bx.psu.edu/~rxc48/dsk-1.6333.tar.gz

Genouest.org is having IT troubles but they should be back up soon...
Forum: Bioinformatics 08-25-2013, 05:13 PM
Replies: 4
Views: 1,701
Posted By rchikhi
Hello, I regret that you had issues running...

Hello,

I regret that you had issues running DSK. You were on the right track though.
If anyone reads this and wonders what the answers to his questions are:

The input data needs not be FASTA....
Forum: Bioinformatics 06-03-2013, 01:55 PM
Replies: 2
Views: 1,224
Posted By rchikhi
As an author of Minia, I would say that it looks...

As an author of Minia, I would say that it looks good, but I would be a bit biased :) Thanks for using the software.

The k=73 min_abundance=2 assembly appears to be better than the k=63...
Forum: Bioinformatics 06-02-2013, 03:13 PM
Replies: 3
Views: 2,805
Posted By rchikhi
I sometimes observe that SOAPdenovo contigs (not...

I sometimes observe that SOAPdenovo contigs (not scaffolds) tend to assemble more than the genome size. Did you run a Velvet assembly, and if so, what was the assembly size?
Forum: De novo discovery 04-01-2013, 06:31 AM
Replies: 15
Views: 5,953
Posted By rchikhi
Hi, Minia has been tested exclusively on Illumina...

Hi, Minia has been tested exclusively on Illumina data. It does not handle color-space reads. If you have color-space, you could always convert the reads to FASTA and feed them to Minia (but then the...
Forum: De novo discovery 02-13-2013, 08:03 AM
Replies: 15
Views: 5,953
Posted By rchikhi
Yes, you can run a couple of Minia's at the same...

Yes, you can run a couple of Minia's at the same time. (using `parallel` or just some terminal windows..)

Given that the first step of Minia becomes limited by your hard drive speed, I would not...
Forum: Bioinformatics 02-02-2013, 03:25 PM
Replies: 1
Views: 1,285
Posted By rchikhi
I communicated via private messages with yun. ...

I communicated via private messages with yun.

I checked a human assembly made with Minia, and indeed, the first contigs outputted often start with polyA. This is not an artifact of yun's data. It...
Forum: De novo discovery 01-07-2013, 05:41 AM
Replies: 5
Views: 2,271
Posted By rchikhi
Did you try running Velvetg with "-exp_cov auto"...

Did you try running Velvetg with "-exp_cov auto" instead of "-exp_cov 227"?
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