Survey of MapReduce frame operation in bioinformatics

Fractal MapReduce decomposition of sequence alignment

(2012) Jonas S Almeida et al.   Algorithms for Molecular Biology

FX: an RNA-Seq analysis tool on the cloud

(2012) Dongwan Hong et al.   BIOINFORMATICS

Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses

(2012) Laurent Jourdren et al.   BIOINFORMATICS

SOAP3: ultra-fast GPU-based parallel alignment tool for short reads

(2012) C.-M. Liu et al.   BIOINFORMATICS

Cloud computing for comparative genomics

(2012) Dennis P Wall et al.   BMC BIOINFORMATICS

FTSite: high accuracy detection of ligand binding sites on unbound protein structures

(2011) Chi-Ho Ngan et al.   BIOINFORMATICS

SEAL: a distributed short read mapping and duplicate removal tool

(2011) L. Pireddu et al.   BIOINFORMATICS

Gene set analysis in the cloud

(2011) L. Zhang et al.   BIOINFORMATICS

PeakRanger: A cloud-enabled peak caller for ChIP-seq data

(2011) Xin Feng et al.   BMC BIOINFORMATICS

SAMQA: error classification and validation of high-throughput sequenced read data

(2011) Thomas Robinson et al.   BMC GENOMICS

GPU-BLAST: using graphics processors to accelerate protein sequence alignment

(2010) P. D. Vouzis et al.   BIOINFORMATICS

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Phenotypic connections in surprising places

(2010) Bolan Linghu et al.   GENOME BIOLOGY

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

Updates to the RMAP short-read mapping software

(2009) A. D. Smith et al.   BIOINFORMATICS

CloudBurst: highly sensitive read mapping with MapReduce

(2009) M. C. Schatz   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

Searching for SNPs with cloud computing

(2009) Ben Langmead et al.   GENOME BIOLOGY