High-quality genome sequences of uncultured microbes by assembly of read clouds

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Genome-wide reconstruction of complex structural variants using read clouds

(2017) Noah Spies et al.   NATURE METHODS

Haplotyping germline and cancer genomes with high-throughput linked-read sequencing

(2016) Grace X Y Zheng et al.   NATURE BIOTECHNOLOGY

TruSPAdes: barcode assembly of TruSeq synthetic long reads

(2016) Anton Bankevich et al.   NATURE METHODS

Assembly of long error-prone reads using de Bruijn graphs

(2016) Yu Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments

(2016) Y. He et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes

(2016) Richard Allen White et al.   mSystems

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Read clouds uncover variation in complex regions of the human genome

(2015) Alex Bishara et al.   GENOME RESEARCH

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms

(2015) Itai Sharon et al.   GENOME RESEARCH

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

SIP metagenomics identifies uncultivated Methylophilaceae as dimethylsulphide degrading bacteria in soil and lake sediment

(2015) Özge Eyice et al.   ISME Journal

Unusual biology across a group comprising more than 15% of domain Bacteria

(2015) Christopher T. Brown et al.   NATURE

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

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

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

(2015) Nicholas J Loman et al.   NATURE METHODS

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria

(2015) Brett J Baker et al.   Microbiome

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei

(2014) Michael T. Leonard et al.   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

(2014) Yu-Wei Wu et al.   Microbiome

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

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

The genome sequence of the colonial chordate, Botryllus schlosseri

(2013) Ayelet Voskoboynik et al.   eLife

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

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS