Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations

A two-phase binning algorithm using l-mer frequency on groups of non-overlapping reads

(2015) Le Vinh et al.   Algorithms for Molecular Biology

Clustering of reads with alignment-free measures and quality values

(2015) Matteo Comin et al.   Algorithms for Molecular Biology

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection

(2015) Xiao Ding et al.   BMC BIOINFORMATICS

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

(2015) Rachid Ounit et al.   BMC GENOMICS

Multi-Layer and Recursive Neural Networks for Metagenomic Classification

(2015) Gregory Ditzler et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Cloud Computing-Based TagSNP Selection Algorithm for Human Genome Data

(2015) Che-Lun Hung et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Bioinformatics on the Cloud Computing Platform Azure

(2014) Hugh P. Shanahan et al.   PLoS One

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

(2013) André Schumacher et al.   BIOINFORMATICS

Scalable metagenomic taxonomy classification using a reference genome database

(2013) Sasha K. Ames et al.   BIOINFORMATICS

Alignment-free supervised classification of metagenomes by recursive SVM

(2013) Hongfei Cui et al.   BMC GENOMICS

Survey of MapReduce frame operation in bioinformatics

(2013) Q. Zou et al.   BRIEFINGS IN BIOINFORMATICS

Cloud computing for comparative genomics

(2012) Dennis P Wall et al.   BMC BIOINFORMATICS

Metagenomic abundance estimation and diagnostic testing on species level

(2012) Martin S. Lindner et al.   NUCLEIC ACIDS RESEARCH

METAGENOMIC TAXONOMIC CLASSIFICATION USING EXTREME LEARNING MACHINES

(2012) ZEEHASHAM RASHEED et al.   Journal of Bioinformatics and Computational Biology

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

(2011) Ronald C Taylor   BMC BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparison of Statistical Methods to Classify Environmental Genomic Fragments

(2010) G L Rosen et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

MapReduce

(2009) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

MapReduce

(2008) Jeffrey Dean et al.   COMMUNICATIONS OF THE ACM