ExSPAnder: a universal repeat resolver for DNA fragment assembly

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment

(2013) John Kececioglu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Dirichlet Mixtures, the Dirichlet Process, and the Structure of Protein Space

(2013) Viet-An Nguyen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells

(2011) Yang Chen et al.   BIOINFORMATICS

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Paired de Bruijn Graphs: A Novel Approach for Incorporating Mate Pair Information into Genome Assemblers

(2011) Paul Medvedev et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies

(2010) Sébastien Boisvert et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ABySS: A parallel assembler for short read sequence data

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

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)

(2009) Alla Lapidus et al.   Standards in Genomic Sciences

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH