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Update to use SKA2
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nickjcroucher committed May 5, 2023
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Expand Up @@ -10,10 +10,10 @@ tar xfz PMEN3_assemblies.tar.gz

## Generating the alignment

The draft genomes can be aligned to the reference using [SKA](https://github.com/simonrharris/SKA). This is first installed through conda:
The draft genomes can be aligned to the reference using [SKA2](https://github.com/bacpop/ska.rust). This is first installed through conda:

```
conda install -c bioconda ska
conda install -c bioconda ska2
```

An index file is then generated to name the isolates to be aligned:
Expand All @@ -38,7 +38,7 @@ The `PMEN3_isolates.list` should contain this text:
The alignment is then constructed using the Gubbins script `generate_ska_alignment.py`:

```
generate_ska_alignment.py --reference RMV4.fa --fasta PMEN3_isolates.list --out PMEN3.aln
generate_ska_alignment.py --reference RMV4.fa --input PMEN3_isolates.list --out PMEN3.aln
```

## Analysis with Gubbins
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