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Application data

Biological application domain(s) Sequence assembly (de novo assembly)
Principal bioinformatics method(s) Sequence assembly, Read mapping
Technology 454, Sanger, Ion Torrent
Created at 454 Life Sciences
Maintained? Yes
Input format(s) SFF, FASTA, FASTQ
Output format(s) FASTA, QUAL, ACE, AGP, BAM
Programming language(s) C++
Licence Unknown
Operating system(s) Linux 64

Summary: The assembly/mapping program developed by 454 Life Sciences for of 454 data

Newbler is in fact the core of both the gsAssembler/GS De Novo Assembler (GUI based), gsMapper/GS Reference Mapper Software /Gui based), runAssembly (command-line based) and gsMapper (command-line based). It uses k-mer based hashing and the 'overlap-layout-consensus' approach. Takes both shotgun and paired end reads.

Latest stable version is 2.6, which allows for the direct incorporation of Illumina fastq files (with mate-pair recognition), including those from the Sequence Read Archive. The sff files produced by the Ion Torrent platform are compatible with newbler.



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