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medaka-software [2019/09/04 01:12] (current)
aorth created
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 +====== medaka ======
 +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: 0.8.2
 +  * Added: September, 2019
 +  * Link: https://​github.com/​nanoporetech/​medaka
 +
 +===== Usage =====
 +Show all available versions of medaka:
 +<​code>​$ module avail medaka</​code>​
 +
 +Load a particular version of medaka into your environment and run it:
 +
 +<​code>​$ module load medaka/​0.8.2
 +$ medaka</​code>​
 +
 +===== Installation =====
 +Notes from the sysadmin during installation:​
 +
 +<​code>​$ sudo mkdir -p /​export/​apps/​medaka/​v0.8.2
 +$ sudo chown aorth /​export/​apps/​medaka/​v0.8.2
 +$ python3 -m venv /​export/​apps/​medaka/​v0.8.2
 +$ source /​export/​apps/​medaka/​v0.8.2/​bin/​activate
 +$ pip install --upgrade pip setuptools
 +$ pip install medaka
 +$ sudo chown -R root:root </​code>​
 +
 +This uses the CentOS 7 system'​s Python 3.6 environment.
medaka-software.txt · Last modified: 2019/09/04 01:12 by aorth