From 560591e12e1fbc8bd469bcc4b24d3a858abb89da Mon Sep 17 00:00:00 2001
From: Emory Hufbauer <mindoftea@gmail.com>
Date: Fri, 17 Dec 2021 07:13:42 -0800
Subject: [PATCH] updated minimap2 options for omicron

---
 bjorn.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bjorn.smk b/bjorn.smk
index b4a31fe..4a03e18 100644
--- a/bjorn.smk
+++ b/bjorn.smk
@@ -107,7 +107,7 @@ rule align_to_reference:
     threads: max_task_cpus
     shell:
         """
-        minimap2 -a -x asm5 --sam-hit-only --secondary=no -t{max_task_cpus} {reference_fp} {input} |
+        minimap2 -a -x asm20 --score-N=0 --sam-hit-only --secondary=no -t{max_task_cpus} {reference_fp} {input} |
             gofasta sam toMultiAlign -t{max_task_cpus} --reference {reference_fp} --trimstart 265 --trimend 29674 --trim --pad |
             python/msa_2_mutations.py -r '{patient_zero}' -d '{data_source}' -i /dev/stdin -o {output}
         """