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.
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:
License: Site license.
No experts have currently registered expertise on this specific subject. List of registered field experts:
| || ||Field||AE FTE||General activities|
|Anders Hast (UPPMAX)||UPPMAX||Visualisation, Digital Humanities||30||Software and usability for projects in digital humanities|
|Anders Sjölander (UPPMAX)||UPPMAX||Bioinformatics||100||Bioinformatics support and training, job efficiency monitoring, project management|
|Anders Sjöström (LUNARC)||LUNARC||GPU computing|
|50||Helps users with MATLAB, General programming, Image processing, Usage of clusters|
|Birgitte Brydsö (HPC2N)||HPC2N||Parallel programming|
|Training, general support|
|Björn Claremar (UPPMAX)||UPPMAX||Meteorology, Geoscience||100||Support for geosciences, Matlab|
|Björn Viklund (UPPMAX)||UPPMAX||Bioinformatics|
|100||Bioinformatics, containers, software installs at UPPMAX|
|Chandan Basu (NSC)||NSC||Computational science||100||EU projects IS-ENES and PRACE.|
Working on climate and weather codes
|Diana Iusan (UPPMAX)||UPPMAX||Computational materials science|
|50||Compilation, performance optimization, and best practice usage of electronic structure codes.|
|Frank Bramkamp (NSC)||NSC||Computational fluid dynamics||100||Installation and support of computational fluid dynamics software.|
|Hamish Struthers (NSC)||NSC||Climate research||80||Users support focused on weather and climate codes.|
|Henric Zazzi (PDC)||PDC||Bioinformatics||100||Bioinformatics Application support|
|Jens Larsson (NSC)||NSC||Swestore|
|Jerry Eriksson (HPC2N)||HPC2N||Parallel programming|
|HPC, Parallel programming|
|Joachim Hein (LUNARC)||LUNARC||Parallel programming|
Parallel programming support
|Johan Hellsvik||PDC||Materialvetenskap||30||materials theory, modeling of organic magnetic materials,|
|Johan Raber (NSC)||NSC||Computational chemistry||50|
|Jonas Lindemann (LUNARC)||LUNARC||Grid computing|
|20||Coordinating SNIC Emerging Technologies|
Developer of ARC Job Submission Tool
Grid user documentation
Leading the development of ARC Storage UI
Lunarc HPC Desktop
|Krishnaveni Chitrapu (NSC)||NSC||Software development|
|Lars Eklund (UPPMAX)||UPPMAX||Chemistry|
|100||Chemistry codes, databases at UPPMAX, sensitive data, PUBA agreements|
|Lars Viklund (HPC2N)||HPC2N||General programming|
|HPC, General programming, installation of software, support, containers|
|Lilit Axner (PDC)||PDC||Computational fluid dynamics||50|
|Marcus Lundberg (UPPMAX)||UPPMAX||Computational science|
|100||I help users with productivity, program performance, and parallelisation.|
|Martin Dahlö (UPPMAX)||UPPMAX||Bioinformatics||10||Bioinformatic support|
|Mikael Djurfeldt (PDC)||PDC||Neuroinformatics||100|
|Mirko Myllykoski (HPC2N)||HPC2N||Parallel programming|
|Parallel programming, HPC, GPU programming, advanced support|
|Pavlin Mitev (UPPMAX)||UPPMAX||Computational materials science||100|
|Pedro Ojeda-May (HPC2N)||HPC2N||Molecular dynamics|
|Training, HPC, Quantum Chemistry, Molecular dynamics, R, advanced support|
|Peter Kjellström (NSC)||NSC||Computational science||100||All types of HPC Support.|
|Peter Münger (NSC)||NSC||Computational science||60||Installation and support of MATLAB, Comsol, and Julia.|
|Rickard Armiento (NSC)||NSC||Computational materials science||40||Maintainer of the scientific software environment at NSC.|
|Szilard Pall||PDC||Molecular dynamics||55||Algorithms & methods for accelerating molecular dynamics, Parallelization and acceleration of molecular dynamics on modern high performance computing architectures, High performance computing, manycore and heterogeneous architectures, GPU computing|
|Thomas Svedberg (C3SE)||C3SE||Solid mechanics|
|Tom Langborg (NSC)||NSC||Swestore|
|Torben Rasmussen (NSC)||NSC||Computational chemistry||100||Installation and support of computational chemistry software.|
|Wei Zhang (NSC)||NSC||Computational science|
|code optimization, parallelization.|
|Weine Olovsson (NSC)||NSC||Computational materials science||90||Application support, installation and help|
|Åke Sandgren (HPC2N)||HPC2N||Computational science||50||SGUSI|