About This Project¶
This pipeline was developed as part of the SARS-2 Bioinformatics & Data Science course offered jointly by Freie Universität Berlin and the Robert Koch Institute.
Objectives¶
The aim was to create a reproducible, modular, and fully-documented pipeline for assembling and analyzing SARS-CoV-2 genomes from Illumina paired-end sequencing data using best-practice bioinformatics tools.
Author¶
Abhinav Mishra
Email: mishraabhinav@gmail.com
Instructors¶
- Max von Kleist, Robert Koch Institute
- Martin Hölzer, Freie Universität Berlin
Course Info¶
You can view on GitHub
Device and Environment Tested On¶
Report details¶
- Date generated: 2025-12-16 20:43:27
Hardware Information:¶
- Hardware Model: Dell Inc. OptiPlex 3050
- Memory: 32.0 GiB
- Processor: Intel® Core™ i7-6700 × 8
- Graphics: Intel® HD Graphics 530 (SKL GT2)
- Disk Capacity: 1.0 TB
Software Information:¶
- Firmware Version: 1.31.0
- OS Name: Fedora Linux 43 (Workstation Edition)
- OS Build: (null)
- OS Type: 64-bit
- GNOME Version: 49
- Windowing System: Wayland
- Kernel Version: Linux 6.17.11-300.fc43.x86_64
Execution Results¶
Below are the two execution result tables in Markdown format.
1. Resource Usage by Process¶
| Process Name | Count | Avg Duration | Max Duration | Avg Memory (RSS) | Max Memory (RSS) | Avg CPU |
|---|---|---|---|---|---|---|
| downloadData | 1 | 26.4s | 26.4s | 27.0 MB | 27.0 MB | 30.1% |
| referenceGenome | 1 | 889ms | 889ms | 12.0 MB | 12.0 MB | 8.7% |
| qc | 2 | 2m 45s | 2m 45s | 2.45 GB | 2.8 GB | 208.7% |
| mapping | 2 | 19.4s | 19.5s | 722.5 MB | 727.0 MB | 312.1% |
| primerClipping | 2 | 1.8s | 2.0s | 50.1 MB | 50.9 MB | 100.9% |
| variantCalling | 2 | 1.3s | 1.3s | 10.4 MB | 10.5 MB | 99.1% |
| consensusGeneration | 2 | 370ms | 385ms | 3.0 MB | 3.0 MB | 3632.5% |
| mergeConsensus | 1 | 225ms | 225ms | 0 MB | 0 MB | 0% |
| phylogeny | 1 | 1.1s | 1.1s | 6.8 MB | 6.8 MB | 0% |
2. Detailed Task Execution Table¶
| Task ID | Process | Status | Realtime | %CPU | Peak Memory |
|---|---|---|---|---|---|
| 1 | referenceGenome | COMPLETED | 784ms | 8.7% | 12 MB |
| 2 | downloadData | COMPLETED | 26.3s | 30.1% | 27 MB |
| 3 | qc (200408_20-04246...) | COMPLETED | 1m 4s | 162.3% | 2.1 GB |
| 5 | qc (200423_20-04411...) | COMPLETED | 2m 44s | 255.0% | 2.8 GB |
| 6 | mapping (200408_20-04246...) | COMPLETED | 19.4s | 315.6% | 718 MB |
| 8 | mapping (200423_20-04411...) | COMPLETED | 19.5s | 308.5% | 727 MB |
| 9 | primerClipping (200408...) | COMPLETED | 2.0s | 102.6% | 50.9 MB |
| 10 | primerClipping (200423...) | COMPLETED | 1.6s | 99.1% | 49.3 MB |
| 11 | variantCalling (200408...) | COMPLETED | 1.3s | 98.8% | 10.4 MB |
| 12 | variantCalling (200423...) | COMPLETED | 1.2s | 99.3% | 10.5 MB |
| 13 | consensusGeneration | COMPLETED | 385ms | 4538.1% | 3 MB |
| 14 | mergeConsensus | COMPLETED | 225ms | 0% | 0 MB |
| 15 | phylogeny | COMPLETED | 1.1s | 0% | 6.8 MB |
Acknowledgments¶
Special thanks to the course instructors and the contributing open-source bioinformatics community whose tools made this project possible.
License¶
This work is licensed under the BSD 3-Clause License.
For a list of references, see references.md.