Getting Newbler

[animesh]

Is there any demo copy available for Newbler?

[zgyzsl]

yes, I am interested in this assembler too.who can give us a reply.

[bioinfosm]

I think you only get it if you have a 454... (with all the licensing, etc)

[Layla]

yes this is true. If you have the 454 software with the licence then you can use it

[dan]

What is the alternative?

[Layla]

There are other commercial software available to analyse your 454 without using gsMapper/DeNovo or gsAssembler. The only one I can currently remember is Biogene

[dan]

I was specifically thinking of non commercial tools. I think I'll try the wgs-assembler (Celera assembler).

Cheers,

[sklages]

wgs-assembler makes a good job on sanger, FLX and Titanium data either alone
or as hybrid assemblies ..

It is not working with short read data (illiumina, solid) and is not optimised for
old gs20 data.

cheers,
Sven

[strob]

If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.

[v_kisand]

MIRA should be nice alternative as well. I would go on wgs or MIRA ... or check velvet... in my mind these three are the most promising. I tested a bit CLC Genome Workbench and was not particularly impressed...

If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.

[sram]

Not so here in Chile...

If you use 454 data you can just ask for the Newbler software. We did it this way and we received a DVD containing everything we need.

I did that and I was told I can get the software only if I have a GS FLX system. I get this answer from a representant of Roche here in Chile.

---sram

[dan]

I really have no idea why Roche insist that only people with the sequencer are allowed the software... They are actively damaging their software's status among the bioinformatics community.

Seriously, what do they expect? Only sequencing centres will do bioinf analysis with 454 data? Clearly not. Therefore we are forced by Roche NOT to use Roche products... What kind of crazy logic is that?

Dear Roche,

Please make Newbler open source immediately.

Sincerely,

Someone who imagines that you actually care about improving your software and increasing its user base.


sram, try writing to the people who gave you the data, and ask them to ask Roach on your behalf.

[strob]

Again, I had no trouble getting the software. They just asked me where we get our sequences from (which provider), and a few days later the DVD's were in my mailbox....

[sram]

I really have no idea why Roche insist that only people with the sequencer are allowed the software... They are actively damaging their software's status among the bioinformatics community.

Seriously, what do they expect? Only sequencing centres will do bioinf analysis with 454 data? Clearly not. Therefore we are forced by Roche NOT to use Roche products... What kind of crazy logic is that?

Dear Roche,

Please make Newbler open source immediately.

Sincerely,

Someone who imagines that you actually care about improving your software and increasing its user base.


sram, try writing to the people who gave you the data, and ask them to ask Roach on your behalf.

Dan, thank you. I will do that. I am receiving the data from research centres in Europe who work with us in some projects. In fact some samples are ours and they are supporting us with the sequencing. Perhaps Roche have a different policy in Europe.. taking in account the message from strob, who appear to be writing from Belgium.
I totally agree with you about Roche should make this software available for academic research. For commercial uses is another thing.

---sram

[strob]

I work indeed in Belgium, Europe. And I even work in a commercial company....

At the PAG meeting I discussed this with Roche at their booth and they just told me that I should contact my local contact. After 1 phone cal, I received the software.