From 21e70def99edad2d47c150c3ed291ad11350a2d3 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Fri, 5 May 2023 08:14:44 +0100 Subject: [PATCH] Update to use SKA2 --- docs/gubbins_tutorial.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/gubbins_tutorial.md b/docs/gubbins_tutorial.md index 7b5baf0d..0137915a 100644 --- a/docs/gubbins_tutorial.md +++ b/docs/gubbins_tutorial.md @@ -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: @@ -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