Bioscope
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 | ||
|---|---|---|---|---|
| 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 MATLAB General programming Technical acoustics | 50 | Helps users with MATLAB, General programming, Image processing, Usage of clusters |
| Birgitte Brydsö (HPC2N) | HPC2N | Parallel programming HPC | Training, general support | |
| Björn Claremar (UPPMAX) | UPPMAX | Meteorology, Geoscience | 100 | Support for geosciences, Matlab |
| Björn Viklund (UPPMAX) | UPPMAX | Bioinformatics Containers | 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 Performance tuning | 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 | HPC, Parallel programming | |
| Joachim Hein (LUNARC) | LUNARC | Parallel programming Performance optimisation | 85 | HPC training Parallel programming support Performance optimisation |
| 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 Desktop environments | 20 | Coordinating SNIC Emerging Technologies Developer of ARC Job Submission Tool Grid user documentation Leading the development of ARC Storage UI Lunarc Box Lunarc HPC Desktop |
| Krishnaveni Chitrapu (NSC) | NSC | Software development | ||
| Lars Eklund (UPPMAX) | UPPMAX | Chemistry Data management FAIR Sensitive data | 100 | Chemistry codes, databases at UPPMAX, sensitive data, PUBA agreements |
| Lars Viklund (HPC2N) | HPC2N | General programming HPC | HPC, General programming, installation of software, support, containers | |
| Lilit Axner (PDC) | PDC | Computational fluid dynamics | 50 | |
| Marcus Lundberg (UPPMAX) | UPPMAX | Computational science Parallel programming Performance tuning Sensitive data | 100 | I help users with productivity, program performance, and parallelisation. I also work with allocations and with sensitive data questions |
| Martin Dahlö (UPPMAX) | UPPMAX | Bioinformatics | 10 | Bioinformatic support |
| Matias Piqueras (UPPMAX) | UPPMAX | Humanities, Social sciences | 70 | Support for humanities and social sciences, machine learning |
| Mikael Djurfeldt (PDC) | PDC | Neuroinformatics | 100 | |
| Mirko Myllykoski (HPC2N) | HPC2N | Parallel programming GPU computing | Parallel programming, HPC, GPU programming, advanced support | |
| Pavlin Mitev (UPPMAX) | UPPMAX | Computational materials science | 100 | |
| Pedro Ojeda-May (HPC2N) | HPC2N | Molecular dynamics Machine learning Quantum Chemistry | 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 | ||
| Torben Rasmussen (NSC) | NSC | Computational chemistry | 100 | Installation and support of computational chemistry software. |
| Wei Zhang (NSC) | NSC | Computational science Parallel programming Performance optimisation | code optimization, parallelization. | |
| Weine Olovsson (NSC) | NSC | Computational materials science | 90 | Application support, installation and help |
| Åke Sandgren (HPC2N) | HPC2N | Computational science | 50 | SGUSI |
