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| Function | Algorithm | Description |
|
|
Genomic sequence mapping | CloudAligner [70] | A MapReduce-based application for mapping short reads generated by the next-generation sequencing machines. URL: http://cloudaligner.sourceforge.net/ |
| CloudBurst [71] | A parallel read mapping algorithm used for mapping next-generation sequence data to the human genome and other genomes.
URL: http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst |
| SEAL [72] | A suite of distributed applications for aligning, manipulating, and analysing short DNA reads.
URL: http://biodoop-seal.sourceforge.net/ |
| BlastReduce [73] | A parallel short DNA sequence read mapping algorithm optimized for aligning sequence data for use in SNP discovery, genotyping, and personal genomics. URL: http://www.cbcb.umd.edu/software/blastreduce/ |
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Genomic sequencing analysis | Crossbow [74] | A scalable software pipeline, which combines Bowtie and SoapsSNP for whole genome resequencing analysis. URL: http://bowtie-bio.sourceforge.net/crossbow/index.shtml |
| Contrail [75] | An algorithm for de novo assembly of large genomes from short sequencing reads. Contrail relies on the graph-theoretic framework of de Bruijn graphs. URL: http://sourceforge.net/apps/mediawiki/contrail-bio/index.php?title=Contrail |
| CloudBrush [76] | A distributed genome assembler based on string graphs. URL: https://github.com/ice91/CloudBrush. |
|
| RNA sequencing analysis | Myrna [77] | A cloud computing pipeline for calculating differential gene expression in large RNA-Seq data sets. URL: http://bowtie-bio.sourceforge.net/myrna/index.shtml |
| FX [78] | RNA sequence analysis tool for the estimation of gene expression levels and genomic variant calling. URL: http://fx.gmi.ac.kr/ |
| Eoulsan [79] | An integrated and flexible solution for RNA sequence data analysis of differential expression. URL: http://transcriptome.ens.fr/eoulsan/ |
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Sequence file management | Hadoop-BAM [80] | A novel library for scalable manipulation of aligned next-generation sequencing data in the Hadoop distributed computing framework. URL: http://sourceforge.net/projects/hadoop-bam/ |
| SeqWare [81] | A tool set used to work with next generation genome sequencing technologies (Illumina, ABI SOLiD, 454) which includes a LIMS, Pipeline, and Query Engine. URL: http://sourceforge.net/projects/seqware/ |
| GATK [82] | A MapReduce framework for analysing next-generation DNA sequencing data. URL: http://genome.cshlp.org/content/20/9/1297 |
|
| Phylogenetic analysis | MrsRF [83] | A scalable, efficient multicore algorithm that uses MapReduce to quickly calculate the all-to-all Robinson-Foulds (RF) distance between large numbers of trees. URL: https://code.google.com/p/mrsrf/ |
| Nephele [84] | A set of tools, which use the complete composition vector algorithm in order to group sequence clustering into genotypes based on a distance measure. URL: https://code.google.com/p/nephele/ |
|
| GPU bioinformatics software | GPU-BLAST [85] | An accelerated version of NCBI-BLAST which uses general purpose graphics processing unit (GPU), designed to rapidly manipulate and alter memory to accelerate overall algorithm processing. URL: http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html |
| SOAP3 [86] | Short sequence read alignment algorithm that uses the multiprocessors in a graphic processing unit to achieve ultrafast alignments. URL: http://soap.genomics.org.cn/soap3.html |
|
| Search engine implementation | Hydra [87] | A protein sequence database search engine specifically designed to run efficiently on the Hadoop MapReduce framework. URL: http://www.webcitation.org/query.php?url=http://code.google.com/p/hydra-proteomics/&refdoi=10.1186/1471-2105-13-324 |
| CloudBlast [88] | Scalable BLAST in the cloud. URL: http://ammatsun.acis.ufl.edu/amwiki/index.php/CloudBLAST_Project |
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Miscellaneous | PeakRanger [89] | A multipurpose, ultrafast ChIP sequence peak caller. URL: http://ranger.sourceforge.net/ |
| YunBe [90] | A gene set analysis algorithm for biomarker identification in the cloud. URL: http://lrcv-crp-sante.s3-website-us-east-1.amazonaws.com/ |
| BioDoop [91] | A set of tools which modules for handling FASTA streams, wrappers for BLAST, converting sequences to the different formats, and so on. URL: http://dc.crs4.it/projects/biodoop |
| BlueSNP [92] | An algorithm for computationally intensive analyses, feasible for large genotype-phenotype datasets. URL: https://github.com/ibm-bioinformatics/BlueSNP |
| Quake [93] | DNA sequence error detection and correction in sequence reads. URL: http://www.cbcb.umd.edu/software/quake/ |
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