Newbler
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Application data |
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| 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
"Error: no local variable "counter" was set." is not a number.
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
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