Hadoop-BAM protocols

View Hadoop-BAM computational protocol

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Hadoop-BAM specifications


Unique identifier OMICS_01051
Name Hadoop-BAM
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Parallelization MapReduce
License MIT License
Computer skills Advanced
Stability Stable
High performance computing Yes
Maintained Yes


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Publication for Hadoop-BAM

Hadoop-BAM in pipeline

PMCID: 4955563
PMID: 27195526
DOI: 10.1155/2016/3617572

[…] processing of many small pieces of data greatly reduces computation time. examples of open-source software developed on the hadoop platform for processing genomic data are crossbow [], gatk [], and hadoop-bam []. challenges to the use of cloud computing for genomic data include the long data transfer times for uploading ngs data files to the cloud, the perceived lack of data security […]

Hadoop-BAM in publications

PMCID: 4897895
PMID: 27267963
DOI: 10.1186/s13742-016-0132-7

[…] bioinformatics problems, and we believe they hold a promising future for large-scale bioinformatics applications. work is being done in this direction, with projects such as adam [], seal [], and hadoop-bam [] providing partial bioinformatics solutions that exploit big data frameworks. notwithstanding these efforts, hadoop and similar frameworks are not compatible with conventional hpc […]

PMCID: 4701021
PMID: 26437432
DOI: 10.3390/brainsci5040419

[…] computations to guarantee precision when neural signal data is used to classify and detect various brain disorders []. another novel aspect utilizing the hadoop distributed file system is the hadoop-bam application presented by niemenmaa et al., where hadoop-bam is a unique and innovative library for the scalable manipulation of next-generation genomic sequencing data. the general […]

PMCID: 4539931
PMID: 26282399
DOI: 10.1186/s13062-015-0071-8

[…] data processing workload with frameworks such as hadoop and spark. to this end, we have participated in development of tools that allow bioinformatics data to be efficiently processed in hadoop: hadoop-bam and seqpig [, ]. this work is continued by integrating hadoop and spark into our iaas environment and providing easy to use interfaces for data intensive computing., the stockholm genomics […]

Hadoop-BAM institution(s)
Aalto University, Department of Information and Computer Science, Aalto, Finland

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