Bioscope

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SOLiD Bioscope Bioscope provides a command line for running application-specific sequence analysis tools. The Bioscope framework enables the user to perform off-instrument secondary and tertiary analyses, and it allows configurable bioinformatics workflows for resequencing (mapping, SNP finding (diBayes), copy number variations, inversions, small indels, large indels) and whole transcriptome analysis (mapping, counting, novel transcript finding, UCSC WIG Files creation) Results will be in GFF v3 and SAM formats. The resulting industry-standard files from Bioscope can be used with third-party visualization and analysis software tools.

Availability

Resource Centre Description
Kalkyl UPPMAX cluster resource of about 21 TFLOPS

Tips and tricks

On UPPMAX/UPPNEX you find bioscope in the module systems on the Kalkyl cluster.

Please type :

module load bioinfo-tools bioscope

To load the module. the command is then

bioscope.sh -A b2010999

To run on Kalkyl you need to specify what project shall be accounted for your job run.

Bioscope integrates to the SLURM queueing  system  there so you only need to start bioscope.sh on a login node.

We recommend you run it in the background by using "noup"

nohup ./run.sh MatoBam_nohup.out

Where run.sh have the run line bioscope.sh -A b2010999 -l MaToBam.log MaToBam.plan

Nohup will run the job in the background and you can monitor the progress by reading the MatoBam_nohup.out.

Bioscope can today use at the most 11 nodes for one bioscope run, and you can at the most start two parallel runs. This is due to the limit in the SLURM system. If you need to run several different bioscope runs. I recommend you running them one after another.

Find attached the user manual to this post you need to be loged in on a registered account to read the attachment..

You can also find some test data on the system under the folder:

/bubo/nobackup/uppnex/bioscopedata

License

License: Site license.

Experts

No experts have currently registered expertise on this specific subject. List of registered field experts:
Field AE FTE General activities
Henric Zazzi (PDC) PDC Bioinformatics 100100 Bioinformatics Application support
Joel Hedlund (NSC) NSC Bioinformatics 00
Martin Dahlö (UPPMAX) UPPMAX Bioinformatics 1010 Bioinformatic support
Sebastian DiLorenzo (UPPMAX) UPPMAX Bioinformatics 5050 National bioinformatic support, NGS tumor data

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