Recycler: an algorithm for detecting plasmids fromde novoassembly graphs

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

ExSPAnder: a universal repeat resolver for DNA fragment assembly

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

A better sequence-read simulator program for metagenomics

(2014) Stephen Johnson et al.   BMC BIOINFORMATICS

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae

(2014) S. Conlan et al.   Science Translational Medicine

Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences

(2014) Val F. Lanza et al.   PLoS Genetics

A method for purifying high quality and high yield plasmid DNA for metagenomic and deep sequencing approaches

(2013) Aya Brown Kav et al.   JOURNAL OF MICROBIOLOGICAL METHODS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

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

Insights into the bovine rumen plasmidome

(2012) A. B. Kav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

(2011) Miguel Pignatelli et al.   PLoS One

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA