Crossbow statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Read alignment SNP detection Bioinformatics workflows chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

Crossbow specifications

Information


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
Requirements
Bowtie, SOAPsnp
High performance computing Yes
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Ben Langmead <>

Additional information


http://bowtie-bio.sourceforge.net/crossbow/manual.shtml

Publication for Crossbow

Crossbow in pipelines

 (5)
2016
PMCID: 4955563
PMID: 27195526
DOI: 10.1155/2016/3617572

[…] []. the parallel 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 […]

2013
PMCID: 3655485
PMID: 23710461
DOI: 10.1155/2013/791051

[…] the readers to the documentation available in the aws website []. , currently, there are some cloud-based programs for the analysis of next-generation sequencing data. these include, among others, crossbow [], rsd-cloud [], myrna [], and cloudburst []. in addition, there are some libraries and packages that support the creation and management of computer clusters in the cloud. to the best […]

2013
PMCID: 3655485
PMID: 23710461
DOI: 10.1155/2013/791051

[…] for ngs data processing. furthermore, various bioinformatics programs are already based on the mapreduce framework and are demonstrated to work using the emr product. examples of these tools include crossbow [], rsd-cloud [], myrna [], and cloudburst []., the client program of elastream can create an emr cluster using the apis of aws from the user's local machine. the creation steps are similar […]

2013
PMCID: 3694645
PMID: 23813006
DOI: 10.1093/bioinformatics/btt215

[…] solution is to align the newly sequenced reads to a single reference genome and then query the genomic variation databases to analyze the mismatches. this approach is used in programs such as crossbow (), varscan (), and others (; ). however, if the reads are misaligned during the first step (e.g. reads spanning a mutation), incorrect mismatch locations will be propagated to the second […]

2010
PMCID: 2904649
PMID: 20622843
DOI: 10.1038/nbt0710-691

[…] frameworks like hadoop. this takes expertise and time. a mitigating factor is that hadoop's “streaming mode” allows existing non-parallel tools to be used as computational steps. for instance, crossbow uses the non-cloud programs bowtie and soapsnp, albeit with some small changes to format intermediate data for the hadoop framework. new parallel programming frameworks, such as dryadlinq […]


To access a full list of citations, you will need to upgrade to our premium service.

Crossbow in publications

 (9)
PMCID: 4709609
PMID: 26839887
DOI: 10.1155/2015/807407

[…] 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 […]

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

[…] web services emr on amazon ec2 instances and gce. paired-end sequence reads of publicly available genomic datasets (escherichia coli cc102 strain and a han chinese male genome) were analysed using crossbow, a genetic annotation tool, on hadoop-based platforms with equivalent system specifications –. a standard analytical pipeline was run simultaneously on both platforms multiple times ( and ). […]

PMCID: 3832998
PMID: 24288665
DOI: 10.1155/2013/185679

[…] 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 […]

PMCID: 3655485
PMID: 23710461
DOI: 10.1155/2013/791051

[…] for the scientists with limited computational power. cloud-based software tools have been developed by the academic community for the analysis of biological sequences. these include, among others, crossbow [], rsd-cloud [], myrna [], and cloudburst []. the life science industry has moved in the same direction and started to support cloud computing as well. interestingly, recent ngs instruments […]

PMCID: 3647537
PMID: 23671843
DOI: 10.1155/2013/614923

[…] and the distributed file system are robust against failure. several sequence analysis tools have been redeveloped as cloud tools based on the hadoop architecture, such as cloudblast [] and crossbow []. therefore, standard online tools can be ported to the cloud architecture. such importing of preexisting tools constitutes the main goal of bioinformatics as a service (baas)., […]


To access a full list of publications, you will need to upgrade to our premium service.

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.

Crossbow reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Crossbow