newbler background

[Tom Bair]

Does anyone have any resources for better understanding newbler?

I have tried to find a primary publication on it but get swamped with papers that are just talking about using it not how it works.

Has any paper/ white paper been published that describes how newbler works?

Thanks

[strob]

same problem here

[flxlex]

This publication gives at least a general description, not too technical:

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.
Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.
BMC Genomics. 2008 Aug 28;9:404. http://www.ncbi.nlm.nih.gov/pubmed/18755037

[hlu]

Does anyone have any resources for better understanding newbler?

I have tried to find a primary publication on it but get swamped with papers that are just talking about using it not how it works.

Has any paper/ white paper been published that describes how newbler works?

Thanks

I am not aware of any publication from 454/Roche on Newbler software.

However, Newbler (or officially called "GS De Novo Assembler") has very thick manual, which gives lots of detailed information on the software. You might want to look up that first to see details.

[hlu]

This publication gives at least a general description, not too technical:

Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.
Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.
BMC Genomics. 2008 Aug 28;9:404. http://www.ncbi.nlm.nih.gov/pubmed/18755037

Things are moving fast. This paper obviously is outdated.

Titanium shotgun is 400bp average length per read, 500 MB per run.

Titanium paired end 3kb, 8kb 20kb is going to be out soon. math all changed with Titanium.

[Tom Bair]

Have the big manual for the newbler stack (gsAssembler et al.) but it deals with running the software, not how it runs. More interested in algorithm than implementation. Thanks for the suggestion though.

[hlu]

Have the big manual for the newbler stack (gsAssembler et al.) but it deals with running the software, not how it runs. More interested in algorithm than implementation. Thanks for the suggestion though.

I see. There is not a lot of public information on the algorithm in the past.

I have attended presentation by Newbler bioinformatics developers in the past. My understanding of this algorithm is that it is based on heuristic intitial index look up up (similar to kmer, or blast algorithm type), then find the the most promising local regions for full blown dynamic programming local alignment.

The original 454 scientific advisor on Newbler was Gene Myers, who was chief at Celera Genomics for the original Celera assembly software, and one of original author of NCBI blast. Newbler originally got a lots of advice and influence of design from Gene Myers.

The current 454 chief on Newbler design is James Knight, director of 454's Bioinformatics Development. One important background, Knight was Ph.D. graduate student of Gene Myers decades ago. Knight gave talk recently at AGBT meeting on Newbler and if you can get hold of his slides there, there might be more information there.

[Tom Bair]

Good information thanks

[Soni]

Newbler manual

Does anyone have a copy of the newbler/GS de novo assembler software user manual? I can't find one on the internet...Cheers.

[bio-x]

Does anyone have a copy of the newbler/GS de novo assembler software user manual? I can't find one on the internet...Cheers.

how to send it to you?

[seb567]

You can read the supplementary methods of the 454 paper. Newbler is described a little there.

http://www.nature.com/nature/journal/v437/n7057/extref/nature03959-s3.doc

http://dx.doi.org/10.1038/nature03959

[flxlex]

In the Materials and Methods section of this paper:

Quinn et al, 2008: Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome

http://www.ncbi.nlm.nih.gov/pubmed/18755037

there is a (limited) description of how newbler works. Newbler stands for 'new assembler', by the way (so they told me).


flxlex