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```
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Can you figure out how to run it? Once you have your protein translations you are ready. Use the HMM.essential.rb script and compare the completeness/contamination to the values you previously obtained using checkM. Why do you think these values are not the same?
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# Quality
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## Anvi’o
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### Installation
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Feel free to explore the anvi’o documentation (it’s really helpful) on the anvi’o website!
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```
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http://merenlab.org/software/anvio/
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```
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We are going to install Anvi'o now:<br>
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Step 1: install miniconda if you don’t have it already:
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```
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$ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
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```
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After the download is finished:
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```
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$ bash Miniconda3-latest-Linux-x86_64.sh
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```
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You will have to enter yes at least once, probably 2 times
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$ source ~/.bashrc
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Step 2: get anvio:
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```
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$ conda update conda
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$ conda create -n anvio-6.1 python=3.6
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$ conda activate anvio-6.1
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$ conda install -y -c conda-forge -c bioconda anvio=6.1
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$ conda install -y diamond=0.9.14
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$ anvi-self-test --suite mini
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```
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###### test doesn't work because of a problem connecting to a web explored
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Activate anvio:
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```
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$ conda activate anvio-6.1
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```
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Anvi'o tutorial: In the day_2 folder on ~/marmic_NGS2019/data you’ll see a directory called anvio_example. Everything you need in order to do an analysis with anvio is in there. The mapping has already been done so don’t worry about that. <br>
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In general the steps to analyze your bins using anvi'o you should follow the following step-by-step:
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```
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Step 1: generate contigs database with anvi-gen-contigs-database <br>
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Step 2: look for single-copy genes with anvi-run-hmms <br>
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Step 3: profile your bam files using anvi-profile <br>
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Step 4: merge your profiles with anvi-merge <br>
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Step 5: visualize your assembly with anvi-interactive.
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```
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To do step 5 you need to open chrome, then go to the web address for your linux-desktop: (change X to your own linux desktop machine)<br>
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```
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http://linux-desktop-X.mpi-bremen.de:8080
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```
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For more info on the anvi'o metagenomic workflow, see: http://merenlab.org/2016/06/22/anvio-tutorial-v2/
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Step 6: use anvi-summarize to summarise your bin collection - now you have all the information you need about your bins :)
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## GTDB-tk
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For this section, we are just going to explore the results for a collection of MAGs previously selected by us. The installation is not hard but it requires too much free space to run. Alternatively, you could also run it using Kbase. However, feel free to install it using conda (these are the instructions from https://github.com/Ecogenomics/GTDBTk).<br>
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