Newbler

From SEQwiki
Jump to: navigation, search

Application data

Biological application domain(s) De-novo assembly
Principal bioinformatics method(s) Assembly, 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.

Links


References

none specified


To add a reference for Newbler, enter the PubMed ID in the field below and click 'Add'.


[ edit box ]

Search for "Newbler" in the SEQanswers forum / BioStar or:

Web Search Wiki Sites Scientific
Personal tools
Namespaces

Variants
Actions
wiki navigation
Software
Toolbox