Evaluation of strategies for the assembly of diverse bacterial genomes using MinION long-read sequencing

Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains

(2018) Luis Acuña-Amador et al.   BMC GENOMICS

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

(2018) Damla Senol Cali et al.   BRIEFINGS IN BIOINFORMATICS

Fusobacterium Genomics Using MinION and Illumina Sequencing Enables Genome Completion and Correction

(2018) S. Michelle Todd et al.   mSphere

Low-Level Antimicrobials in the Medicinal Leech Select for Resistant Pathogens That Spread to Patients

(2018) Lidia Beka et al.   mBio

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

(2017) Sergey Koren et al.   GENOME RESEARCH

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

DNA sequencing at 40: past, present and future

(2017) Jay Shendure et al.   NATURE

antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification

(2017) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Ryan R. Wick et al.   PLoS Computational Biology

The use of Oxford Nanopore native barcoding for complete genome assembly

(2017) Sion C Bayliss et al.   GigaScience

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

Evaluation of hybrid and non-hybrid methods forde novoassembly of nanopore reads

(2016) Ivan Sović et al.   BIOINFORMATICS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Host Matters: Medicinal Leech Digestive-Tract Symbionts and Their Pathogenic Potential

(2016) Jeremiah N. Marden et al.   Frontiers in Microbiology

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

hybridSPAdes: an algorithm for hybrid assembly of short and long reads

(2015) Dmitry Antipov et al.   BIOINFORMATICS

Impact of three Illumina library construction methods on GC bias and HLA genotype calling

(2015) James H. Lan et al.   HUMAN IMMUNOLOGY

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Scaffolding of a bacterial genome using MinION nanopore sequencing

(2015) E. Karlsson et al.   Scientific Reports

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

(2015) Judith Risse et al.   GigaScience

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

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

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

Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case

(2014) Sophie M. Colston et al.   mBio

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation

(2012) Jonathan L Klassen et al.   BMC GENOMICS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA

(2011) Rachel Marine et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons

(2011) Nabil-Fareed Alikhan et al.   BMC GENOMICS

Systematic bias in high-throughput sequencing data and its correction by BEADS

(2011) Ming-Sin Cheung et al.   NUCLEIC ACIDS RESEARCH

ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes

(2011) Alessandro M Varani et al.   GENOME BIOLOGY

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Assembly complexity of prokaryotic genomes using short reads

(2010) Carl Kingsford et al.   BMC BIOINFORMATICS

Read Length and Repeat Resolution: Exploring Prokaryote Genomes Using Next-Generation Sequencing Technologies

(2010) Matt J. Cahill et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis

(2009) Dong-Chan Oh et al.   Nature Chemical Biology