medaka-software
Differences
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| medaka-software [2021/08/25 12:15] – aorth | medaka-software [2025/05/13 12:27] (current) – aorth | ||
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| medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster. | medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster. | ||
| - | * Latest Version: 1.4.3 | + | * Latest Version: 1.12.1 |
| * Added: September, 2019 | * Added: September, 2019 | ||
| - | * Updated: | + | * Updated: |
| * Link: https:// | * Link: https:// | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | Show all available | + | |
| + | Show which versions | ||
| < | < | ||
| Load one version into your environment and run it: | Load one version into your environment and run it: | ||
| - | < | + | < |
| $ medaka -h</ | $ medaka -h</ | ||
| Line 19: | Line 20: | ||
| Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
| - | < | + | < |
| - | $ sudo chown -R aorth:aorth / | + | $ sudo mkdir -p / |
| - | $ module load python/3.7 | + | $ sudo chown aorth / |
| - | $ python3 | + | $ python |
| - | $ source / | + | $ source / |
| - | $ pip install --upgrade | + | $ python -m pip install -U pip setuptools |
| - | $ pip install medaka==1.4.3 | + | $ python -m pip install medaka==1.12.1 |
| - | $ sudo chown -R root:root / | + | $ sudo chown -R root:root / |
medaka-software.1629893755.txt.gz · Last modified: by aorth