CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

Strain/species identification in metagenomes using genome-specific markers

(2014) Qichao Tu et al.   NUCLEIC ACIDS RESEARCH

WGSQuikr: Fast Whole-Genome Shotgun Metagenomic Classification

(2014) David Koslicki et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

GAGE-B: an evaluation of genome assemblers for bacterial organisms

(2013) Tanja Magoc et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ)

(2013) Martin Mascher et al.   PLANT JOURNAL

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space

(2013) Stefano Lonardi et al.   PLoS Computational Biology

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Chromosomes in the flow to simplify genome analysis

(2012) Jaroslav Doležel et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

NBC: the Naive Bayes Classification tool webserver for taxonomic classification of metagenomic reads

(2010) G. L. Rosen et al.   BIOINFORMATICS

Development and implementation of high-throughput SNP genotyping in barley

(2009) Timothy J Close et al.   BMC GENOMICS