An External-Memory Algorithm for String Graph Construction

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly

(2016) Paola Bonizzoni et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Covering Pairs in Directed Acyclic Graphs

(2014) Niko Beerenwinkel et al.   COMPUTER JOURNAL

Space-efficient and exact de Bruijn graph representation based on a Bloom filter

(2013) Rayan Chikhi et al.   Algorithms for Molecular Biology

Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs

(2013) Stefano Beretta et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform

(2012) A. J. Cox et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lightweight algorithms for constructing and inverting the BWT of string collections

(2012) Markus J. Bauer et al.   THEORETICAL COMPUTER SCIENCE

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Trading off space for passes in graph streaming problems

(2010) Camil Demetrescu et al.   ACM Transactions on Algorithms

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH