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Merge branch 'main' of https://github.com/Russel87/MAGinator into main
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trinezac committed Aug 23, 2023
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Expand Up @@ -42,6 +42,12 @@ Run MAGinator:
maginator -v vamb_clusters.tsv -r reads.csv -c contigs.fasta -o my_output -g "/path/to/GTDB-Tk/database/release207_v2/"
```

A testset can be found in the test_data directory.
1. Download the 3 samples used for the test at SRA: https://www.ncbi.nlm.nih.gov/sra?LinkName=bioproject_sra_all&from_uid=715601 with the ID's dfc99c_A, f9d84e_A and 221641_A
2. Change the paths to the read-files in reads.csv
3. Unzip the contigs.fasta.gz
4. Run MAGinator

### Run on a compute cluster
MAGinator can run on compute clusters using qsub (torque), sbatch (slurm), or drmaa structures. The --cluster argument toggles the type of compute cluster infrastructure. The --cluster_info argument toggles the information given to the submission command, and it has to contain the following keywords {cores}, {memory$

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