Newbler
{{short description|Software for DNA sequencing}}
{{Infobox Software
| name = Newbler
| developer = 454 Life Sciences
| operating system = Linux i386/x86_64
| genre = Bioinformatics
| license = Commercial
| latest release version = v2.7
| latest release date = {{Start date and age|2012|2|28}}
}}
Newbler is a software package for de novo DNA sequence assembly. It is designed specifically for assembling sequence data generated by the 454 GS-series of pyrosequencing platforms sold by 454 Life Sciences, a Roche Diagnostics company.{{cite journal|last1=Genivaldo |first1=GZ |last2=Silva|first2=Bas E |last3=Dutilh|first3= David |last4=Matthews|first4=Keri |last5=Elkins|first5=Robert |last6=Schmieder |first6=Elizabeth A |last7=Dinsdale|first7=Robert A Edwards|title=Combining de novo and reference-guided assembly with scaffold_builder|journal=Source Code for Biology and Medicine|volume=8|issue=23|pages=23 |doi=10.1186/1751-0473-8-23|pmid=24267787 |year=2013 |pmc=4177539 |doi-access=free }}
Usage
Newbler can run via a Java GUI (gsAssembler) or the command line (runAssembly). It works natively with the .SFF data output by the sequencer, but is also able to accept FASTA files, containing nucleotide sequences, with or without quality information, and FASTQ files. It will use older Sanger sequence data if appropriately formatted to aid in assembly and scaffolding.
See also
References
{{Reflist}}
External links
- [http://www.my454.com/ 454 Sequencing home page]
Category:Bioinformatics software
Category:Computational science
{{Bioinformatics-stub}}