Newbler is a software package for de novo

De novo

In general usage, de novo is a Latin expression meaning "from the beginning," "afresh," "anew," "beginning again." It is used in:* De novo transcriptome assembly, the method of creating a transcriptome without a reference genome...

DNA sequence assembly

Sequence assembly

In bioinformatics, sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, but rather reads small pieces of between 20 and 1000 bases,...

. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing

Pyrosequencing

Pyrosequencing is a method of DNA sequencing based on the "sequencing by synthesis" principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides...

 platforms sold by 454 Life Sciences

454 Life Sciences

454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...

, a Roche Diagnostics

Roche Diagnostics

Roche Diagnostics Division is a subsidiary of Hoffmann-La Roche which manufactures equipment and reagents for research and medical diagnostic applications. Internally, it is organized into five major business areas: Roche Applied Science, Roche Professional Diagnostics, Roche Diabetes Care, Roche...

 company.

Usage

Newbler can run via a Java GUI

Gui

Gui or guee is a generic term to refer to grilled dishes in Korean cuisine. These most commonly have meat or fish as their primary ingredient, but may in some cases also comprise grilled vegetables or other vegetarian ingredients. The term derives from the verb, "gupda" in Korean, which literally...

 (gsAssembler) or the command line (runAssembly). It works natively with the .SFF data output by the sequencer, but is also able to accept FASTA

FASTA

FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics.- History :...

 files with or without quality information. It will utilise older Sanger sequence data if appropriately formatted to aid in assembly and scaffolding.