iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: http://pubmed.ncbi.nlm.nih.gov/26040456/
Assembling short reads from jumping libraries with large insert sizes - PubMed Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Oct 15;31(20):3262-8.
doi: 10.1093/bioinformatics/btv337. Epub 2015 Jun 3.

Assembling short reads from jumping libraries with large insert sizes

Irina Vasilinetc  1 , Andrey D Prjibelski  2 , Alexey Gurevich  2 , Anton Korobeynikov  3 , Pavel A Pevzner  4
Affiliations

Assembling short reads from jumping libraries with large insert sizes

Irina Vasilinetc et al. Bioinformatics. .

Abstract

Motivation: Advances in Next-Generation Sequencing technologies and sample preparation recently enabled generation of high-quality jumping libraries that have a potential to significantly improve short read assemblies. However, assembly algorithms have to catch up with experimental innovations to benefit from them and to produce high-quality assemblies.

Results: We present a new algorithm that extends recently described exSPAnder universal repeat resolution approach to enable its applications to several challenging data types, including jumping libraries generated by the recently developed Illumina Nextera Mate Pair protocol. We demonstrate that, with these improvements, bacterial genomes often can be assembled in a few contigs using only a single Nextera Mate Pair library of short reads.

Availability and implementation: Described algorithms are implemented in C++ as a part of SPAdes genome assembler, which is freely available at bioinf.spbau.ru/en/spades.

Contact: ap@bioinf.spbau.ru

Supplementary information: Supplementary data are available at Bioinformatics online.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

Publication types