medaka-software
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medaka-software [2019/09/03 22:12] – created aorth | medaka-software [2021/08/25 12:15] (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: | + | * Latest Version: |
* Added: September, 2019 | * Added: September, 2019 | ||
+ | * Updated: August, 2021 | ||
* Link: https:// | * Link: https:// | ||
Line 10: | Line 11: | ||
< | < | ||
- | Load a particular | + | Load one version into your environment and run it: |
- | < | + | < |
- | $ medaka</ | + | $ medaka |
===== Installation ===== | ===== Installation ===== | ||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | + | < |
- | $ sudo chown aorth / | + | $ sudo chown -R aorth:aorth / |
- | $ python3 -m venv / | + | $ module load python/3.7 |
- | $ source / | + | $ python3 -m venv / |
+ | $ source / | ||
$ pip install --upgrade pip setuptools | $ pip install --upgrade pip setuptools | ||
- | $ pip install medaka | + | $ pip install medaka==1.4.3 |
- | $ sudo chown -R root:root </ | + | $ sudo chown -R root: |
- | + | ||
- | This uses the CentOS 7 system' | + |
medaka-software.1567548722.txt.gz · Last modified: 2019/09/03 22:12 by aorth