misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads

PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM and Look Ahead Approach

(2014) Xiao Zhu et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies

(2013) Scott C. Clark et al.   BIOINFORMATICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

CGAL: computing genome assembly likelihoods

(2013) Atif Rahman et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

(2012) K. Chen 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

GemSIM: general, error-model based simulator of next-generation sequencing data

(2012) Kerensa E McElroy et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Mauve Assembly Metrics

(2011) Aaron E. Darling et al.   BIOINFORMATICS

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

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

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

(2011) Paul J. Kersey et al.   NUCLEIC ACIDS RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Sense from sequence reads: methods for alignment and assembly

(2009) Paul Flicek et al.   NATURE METHODS

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

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

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