Crossbow

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]