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Crossbow specifications


Unique identifier OMICS_00284
Name Crossbow
Software type Framework/Library, Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Parallelization MapReduce
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.2.1
Stability Stable
Bowtie, SOAPsnp
High performance computing Yes
Maintained Yes




No version available



  • person_outline Ben Langmead

Additional information

Publication for Crossbow

Crossbow citations


Big Data Analytics for Genomic Medicine

Int J Mol Sci
PMCID: 5343946
PMID: 28212287
DOI: 10.3390/ijms18020412

[…] s lining up the sequence reads to a reference sequence [,] to allow comparison of sequence data from a sample sequenced with the reference genome. A number of alignment tools including CloudBurst [], Crossbow [], and SEAL [] have been developed on Big Data infrastructures. More programs designed for short-read sequence alignment are shown in . Alignment allows a number of quality control (QC) meas […]


Long Read Alignment with Parallel MapReduce Cloud Platform

Biomed Res Int
PMCID: 4709609
PMID: 26839887
DOI: 10.1155/2015/807407

[…] ud environments. A simple MapReduce model deployed on the VM based computing environment is shown in .Next-Generation Sequencing (NGS) tools like CloudAligner [], Cloud Burst [], SeqMapReduce [], and Crossbow [] adopt the Hadoop framework. The major drawback of these alignment tools is that they are short read aligners. The short read aligners prove to be efficient when single-gap or ungapped alig […]


G2LC: Resources Autoscaling for Real Time Bioinformatics Applications in IaaS

PMCID: 4609414
PMID: 26504488
DOI: 10.1155/2015/549026

[…] ning bioinformatics applications on cloud platform.As the field of bioinformatics expands, some researches have utilized cloud computing to deliver large computing capacity and on-demand scalability. Crossbow [] is a cloud enabled tool that combines the aligner Bowtie and the SNP caller SOAPsnp and uses Hadoop for parallel computing. Rainbow [] is a cloud-based software package that can assist in […]


Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets

PLoS One
PMCID: 4172764
PMID: 25247298
DOI: 10.1371/journal.pone.0108490

[…] nt and variant calling, respectively, with GCE being more efficient than EMR. displays the key metrics for data analysis using both services. The proportion of central processing unit (CPU) usage by Crossbow differed between platforms when aligning and SNP calling each genome, with GCE having better utilisation as the genome size increased. There was considerably more free memory on GCE for the s […]


PVT: An Efficient Computational Procedure to Speed up Next generation Sequence Analysis

BMC Bioinformatics
PMCID: 4063226
PMID: 24894600
DOI: 10.1186/1471-2105-15-167

[…] ure of the data centre is shared by a large number of users, reducing the cost to each user. To manage the flood of NGS data, several large-scale computing framework have been implemented in cloud by Crossbow [], Galaxy [] and STORMSeq []. Implementation of TopHat in cloud cannot utilize the cloud resources efficiently due to lack of pipelined execution workflow.Here we propose an efficient execut […]


Enabling Large Scale Biomedical Analysis in the Cloud

Biomed Res Int
PMCID: 3832998
PMID: 24288665
DOI: 10.1155/2013/185679

[…] ab, a suite of tools that allow scientists to orchestrate a sequence of data analysis tasks using remote computing resources and data storage facilities on demand from local devices. Furthermore, the Crossbow [] genotyping program applies the MapReduce workflow on Hadoop to launch many copies of the short-read aligner Bowtie [] in parallel. Once the aligned reads are generated, Hadoop automaticall […]


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Crossbow institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; The iSchool, College of Information Studies, University of Maryland, College Park, MD, USA
Crossbow funding source(s)
Supported in part by NSF grant IIS-0844494, NIH grants R01-LM006845 and R01-HG004885.

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