De novo Assembly of the Brugia malayi Genome Using Long Reads from a Single MinION Flowcell

Epidemiological screening and xenomonitoring for human lymphatic filariasis infection in select districts in the states of Maharashtra and Karnataka, India

(2019) Vishal Khatri et al.   PARASITOLOGY RESEARCH

Elimination within reach: A cross-sectional study highlighting the factors that contribute to persistent lymphatic filariasis in eight communities in rural Ghana

(2019) Corrado Minetti et al.   PLoS Neglected Tropical Diseases

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Comparative genomics of the major parasitic worms

(2018)   NATURE GENETICS

The prevalence of lymphatic filariasis infection and disease following six rounds of mass drug administration in Mandalay Region, Myanmar

(2018) Benjamin F. R. Dickson et al.   PLoS Neglected Tropical Diseases

MinION-based long-read sequencing and assembly extends theCaenorhabditis elegansreference genome

(2017) John R. Tyson et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

(2017) Young-Jun Choi et al.   PLoS Genetics

Detecting and confirming residual hotspots of lymphatic filariasis transmission in American Samoa 8 years after stopping mass drug administration

(2017) Colleen L. Lau et al.   PLoS Neglected Tropical Diseases

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

Population genomics of the filarial nematode parasite Wuchereria bancrofti from mosquitoes

(2016) Scott T. Small et al.   MOLECULAR ECOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Persistent ‘hotspots’ of lymphatic filariasis microfilaraemia despite 14 years of mass drug administration in Ghana

(2016) Nana-Kwadwo Biritwum et al.   TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Programmatic Use of Molecular Xenomonitoring at the Level of Evaluation Units to Assess Persistence of Lymphatic Filariasis in Sri Lanka

(2016) Ramakrishna U. Rao et al.   PLoS Neglected Tropical Diseases

Genomic diversity in Onchocerca volvulus and its Wolbachia endosymbiont

(2016) Young-Jun Choi et al.   Nature Microbiology

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Cessation of Mass Drug Administration for Lymphatic Filariasis in Zanzibar in 2006: Was Transmission Interrupted?

(2015) Maria P. Rebollo et al.   PLoS Neglected Tropical Diseases

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Molecular epidemiology, phylogeny and evolution of the filarial nematode Wuchereria bancrofti

(2014) Scott T. Small et al.   INFECTION GENETICS AND EVOLUTION

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Lymphatic filariasis control in Tanzania: effect of six rounds of mass drug administration with ivermectin and albendazole on infection and transmission

(2013) Paul E Simonsen et al.   BMC INFECTIOUS DISEASES

Persistence of Lymphatic Filarial Infection in the Paediatric Population of Rural Community, after Six Rounds of Annual Mass Drug Administrations

(2013) I. P. Sunish et al.   JOURNAL OF TROPICAL PEDIATRICS

Population Genetics of the Filarial Worm Wuchereria bancrofti in a Post-treatment Region of Papua New Guinea: Insights into Diversity and Life History

(2013) Scott T. Small et al.   PLoS Neglected Tropical Diseases

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The NIH-NIAID Filariasis Research Reagent Resource Center

(2011) Michelle L. Michalski et al.   PLoS Neglected Tropical Diseases

A Deep Sequencing Approach to Comparatively Analyze the Transcriptome of Lifecycle Stages of the Filarial Worm, Brugia malayi

(2011) Young-Jun Choi et al.   PLoS Neglected Tropical Diseases

Interactive microbial genome visualization with GView

(2010) Aaron Petkau et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The genome of Brugia malayi — All worms are not created equal

(2008) Alan L. Scott et al.   PARASITOLOGY INTERNATIONAL