Software used during the course
| Software | Version (if not latest) | Module | Notes |
|---|---|---|---|
| breakdancer | 1.4.5 | ngsbio | |
| samtools | 1.15.1 | ngsbio | |
| bcftools | 1.15.1 | ngsbio | |
| bedtools | 2.30.0 | ngsbio | |
| openmpi | 4.1.4 | ngsbio | |
| r-base | 4.0.5 | ngsbio | |
| bowtie2 | 2.4.5 | ngsbio | |
| macs2 | 2.2.7.1 | ngsbio | |
| meme | 5.4.1 | ngsbio | |
| ucsc-bedgraphtobigwig | 377 | ngsbio | |
| ucsc-fetchchromsizes | 377 | ngsbio | |
| r-sleuth | 0.30.0 | ngsbio | |
| bioconductor-rhdf5 | 2.34.0 | ngsbio | |
| bioconductor-rhdf5filters | 1.2.0 | ngsbio | |
| bioconductor-rhdf5lib | 1.12.0 | ngsbio | |
| hdf5 | 1.10.5 | ngsbio | |
| hisat2 | 2.2.1 | ngsbio | |
| kallisto | 0.46.2 | ngsbio | |
| bwa | 0.7.17 | ngsbio | |
| assembly-stats | 1.0.1 | ngsbio | |
| canu | 2.2 | ngsbio | |
| kmer-jellyfish | 2.3.0 | ngsbio | |
| seqtk | 1.3 | ngsbio | |
| velvet | 1.2.10 | ngsbio | |
| wtdbg | 2.5 | ngsbio | |
| genomescope2 | 2 | ngsbio | |
| freebayes | 0.9.21.7 | ngsbio | |
| gatk4 | 4.2.6.1 | ngsbio | |
| picard-slim | 2.27.4 | ngsbio | |
| minimap2 | 2.24 | ngsbio | |
| sniffles | 2.0.7 | ngsbio | |
| pytz | ngsbio (Python Dependency) | ||
| edlib | ngsbio (Python Dependency) | ||
| threadpoolctl | ngsbio (Python Dependency) | ||
| six | ngsbio (Python Dependency) | ||
| scipy | ngsbio (Python Dependency) | ||
| networkx | ngsbio (Python Dependency) | ||
| joblib | ngsbio (Python Dependency) | ||
| cython | ngsbio (Python Dependency) | ||
| click | ngsbio (Python Dependency) | ||
| scikit-learn | ngsbio (Python Dependency) | ||
| python-dateutil | ngsbio (Python Dependency) | ||
| pandas | ngsbio (Python Dependency) | ||
| lightgbm | ngsbio (Python Dependency) | ||
| sortedcontainers | ngsbio (Python Dependency) | ||
| dysgu | ngsbio (Pip Installation) | ||
| r-ngsplot | chipseq-project | ||
| python | 2.7 | chipseq-project | |
| jupyter | 1.0.0 | jupyter | |
| pandoc | 2.12 | jupyter | |
| bash_kernel | jupyter (Pip Installation) | ||
| texlive-base | jupyter (System Package) | ||
| texlive-xetex | jupyter (System Package) | ||
| texlive-formats-extra | jupyter (System Package) | ||
| texlive-fonts-extra | jupyter (System Package) | ||
| texlive-luatex | jupyter (System Package) | ||
| IGV | 2.14.1 | Standalone |
In this course run we are using Oracle VM Virtual Box (https://www.virtualbox.org/) to deliver Informatics, you can find Virtual Box Guides below:
Virtual Machine Setup Guide.
The Host OS Requirements for Virtual Box
- RAM requirement: 8GB (preferably 12GB)
- Processor requirement: 4 processors (preferably 8)
- Hard disk space: 200GB
- Admin rights to the computer
The course data are free to reuse and adapt with appropriate attribution. All course data in these repositories are licensed under the Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
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