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Forum: Bioinformatics 02-25-2015, 10:16 PM
Replies: 2
Views: 2,800
Posted By ThomasDOtto
Hi all, sorry for never replying to this...

Hi all,

sorry for never replying to this thread, as I have not seen it. Normally people contact me directly.

This reported error is due to the fact that nucmer cannot generate a comparison...
Forum: Bioinformatics 10-10-2013, 07:40 AM
Replies: 5
Views: 3,129
Posted By ThomasDOtto
Well, it might scale ok. All the components are...

Well, it might scale ok. All the components are working fine on large genome, the mapper (SMALT), GATK SNP, and the core icorn should work also. The only thing that won't work would be the checking...
Forum: Bioinformatics 10-10-2013, 06:27 AM
Replies: 5
Views: 3,129
Posted By ThomasDOtto
Icorn2 works on assembled genomes. It is quite...

Icorn2 works on assembled genomes. It is quite powerfull to correct frameshifts that quiver does not correct.
On a 20MB genome, with three iterations and around 100x Illumina coverage it should...
Forum: Bioinformatics 07-29-2013, 04:34 PM
Replies: 1
Views: 1,423
Posted By ThomasDOtto
Dear Siva, we simplified the webpage to find...

Dear Siva,

we simplified the webpage to find the nature protocol that describes the PAGIT tool kit.
http://www.sanger.ac.uk/resources/software/pagit/

Thanks for your interest,
Thomas
Forum: Bioinformatics 07-29-2013, 07:04 AM
Replies: 5
Views: 3,129
Posted By ThomasDOtto
iCORN2 corrects PacBio assemblies

We released iCORN2:
http://icorn.sourceforge.net/

iCORN2 was applied to correct several PacBio assemblies (Bacteria / Plasmodium). It requires short read pairs, and iteratively corrects errors,...
Forum: Bioinformatics 07-29-2013, 05:08 AM
Replies: 5
Views: 3,214
Posted By ThomasDOtto
I just checked the pagit webpage, and indeed it...

I just checked the pagit webpage, and indeed it was not very clear. It should be better now
http://www.sanger.ac.uk/resources/software/pagit/

Thanks,
Thomas
Forum: Bioinformatics 07-29-2013, 04:27 AM
Replies: 1
Views: 1,361
Posted By ThomasDOtto
Hi, does this post resolves the issue? ...

Hi,

does this post resolves the issue?
http://seqanswers.com/forums/showthread.php?p=111933#post111933

Cheers,
Thomas
Forum: Bioinformatics 07-29-2013, 04:27 AM
Replies: 5
Views: 1,897
Posted By ThomasDOtto
Hi, it should be updated now: ...

Hi,

it should be updated now:
http://www.sanger.ac.uk/resources/software/pagit/#Bugs

Basically, download the promer file and replace the old. I did test it here, but this means little...
...
Forum: Bioinformatics 07-29-2013, 03:32 AM
Replies: 5
Views: 3,214
Posted By ThomasDOtto
nature protocol

Hi Siva,

well, there is a nature protocol paper that explains each step:

http://www.nature.com/nprot/journal/v7/n7/full/nprot.2012.068.html
or ...
Forum: Bioinformatics 07-12-2013, 06:22 AM
Replies: 5
Views: 3,214
Posted By ThomasDOtto
Hi, which shell are you using? PAGIT works...

Hi,

which shell are you using? PAGIT works best with the bash shell. Just type
bash
and then repeat the source command.

Cheers,
Thomas
Forum: Bioinformatics 07-12-2013, 06:21 AM
Replies: 2
Views: 1,222
Posted By ThomasDOtto
Sorry for the late reply, and from your other...

Sorry for the late reply, and from your other query I assume to solved the problem.
1) Basically, I don't know how compatible the different versions are. Just give it a go
2) The Virtualbox is the...
Forum: Bioinformatics 07-12-2013, 06:17 AM
Replies: 5
Views: 1,897
Posted By ThomasDOtto
Hi Akjones, it is actually a bug in PAGIT,...

Hi Akjones,

it is actually a bug in PAGIT, that will be fixed in the next version, sorry. The path in the promer file are not consistent with the installation.

Assuming you have sourced the...
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