Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

A comparison of tools for the simulation of genomic next-generation sequencing data

(2016) Merly Escalona et al.   NATURE REVIEWS GENETICS

Bandage: interactive visualization ofde novogenome assemblies: Fig. 1.

(2015) Ryan R. Wick et al.   BIOINFORMATICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

Whole genome sequencing in clinical and public health microbiology

(2015) J.C. Kwong et al.   PATHOLOGY

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

ExSPAnder: a universal repeat resolver for DNA fragment assembly

(2014) A. D. Prjibelski et al.   BIOINFORMATICS

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

(2014) Brian M. Forde et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Molecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258Klebsiella pneumoniae

(2014) Frank R. DeLeo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Reference Genome Sequence of Saccharomyces cerevisiae : Then and Now

(2014) Stacia R. Engel et al.   G3-Genes Genomes Genetics

A comprehensive evaluation of assembly scaffolding tools

(2014) Martin Hunt 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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Ten recommendations for creating usable bioinformatics command line software

(2013) Torsten Seemann   GigaScience

PBSIM: PacBio reads simulator—toward accurate genome assembly

(2012) Yukiteru Ono et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

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

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

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

TubercuList – 10 years after

(2010) Jocelyne M. Lew et al.   TUBERCULOSIS

Genome Sequencing and Comparative Analysis of Klebsiella pneumoniae NTUH-K2044, a Strain Causing Liver Abscess and Meningitis

(2009) K.-M. Wu et al.   JOURNAL OF BACTERIOLOGY

Segment-based multiple sequence alignment

(2008) T. Rausch et al.   BIOINFORMATICS