BASE: a practical de novo assembler for large genomes using long NGS reads - Concepedia

Concepedia

Publication | Open Access

BASE: a practical de novo assembler for large genomes using long NGS reads

DOI Full Paper Access

14

Citations

18

References

2016

Year

Binghang Liu, Chi-Man Liu, Dinghua Li, Yingrui Li, Hing‐Fung Ting, Siu‐Ming Yiu, Ruibang Luo, Tak‐Wah Lam

Abstract

BASE is a practically efficient tool for constructing contig, with significant improvement in quality for long NGS reads. It is relatively easy to extend BASE to include scaffolding.

References

	Year	Citations
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Anton Bankevich, Sergey Nurk, Dmitry Antipov, Journal of Computational Biology	2012	25.9K
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct <i>de Bruijn</i> graph Dinghua Li, Chi-Man Liu, Ruibang Luo, Bioinformatics EngineeringMolecular BiologySoil DataGenomicsSoil Metagenomics	2015	9K
SOAPdenovo2: an empirically improved memory-efficient short-read <i>de novo</i> assembler Ruibang Luo, Binghang Liu, Yinlong Xie, GigaScience	2012	5.5K
IDBA-UD: a <i>de novo</i> assembler for single-cell and metagenomic sequencing data with highly uneven depth Yu Peng, Henry C. M. Leung, Siu‐Ming Yiu, Bioinformatics	2012	3.1K
High-quality draft assemblies of mammalian genomes from massively parallel sequence data Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Proceedings of the National Academy of Sciences	2010	1.6K
Adaptive seeds tame genomic sequence comparison Szymon M. Kiełbasa, Raymond Wan, Kengo Sato, Genome Research	2011	1.4K
Genomic mapping by fingerprinting random clones: A mathematical analysis Eric S. Lander, Michael S. Waterman Genomics Molecular EcologyComparative GenomicsGeneticsMedicineComputational Genomics	1988	975
Efficient de novo assembly of large genomes using compressed data structures Jared T. Simpson, Richard Durbin Genome Research	2011	798
Assemblathon 2: evaluating <i>de novo</i> methods of genome assembly in three vertebrate species Keith Bradnam, Joseph Fass, Anton Alexandrov, GigaScience	2013	723
The fragment assembly string graph Eugene W. Myers Bioinformatics	2005	434

Page 1