From 7ea5a2bd286bbaba94b4b57a0efc4da2b7d9d689 Mon Sep 17 00:00:00 2001
From: SAMtoBAM <31311492+SAMtoBAM@users.noreply.github.com>
Date: Tue, 13 Jan 2026 13:50:22 -0600
Subject: [PATCH] Update fusemblr.sh

---
 bin/fusemblr.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/fusemblr.sh b/bin/fusemblr.sh
index 6b25da2..92e62a3 100644
--- a/bin/fusemblr.sh
+++ b/bin/fusemblr.sh
@@ -259,7 +259,7 @@ echo "Step 1: Downsampling ONT reads"
 mkdir 1.filtlong_ont
 
 ##now run filtlong with the settings
-filtlong --min_length ${minsize} -t ${target} --length_weight ${weight} ${nanoporepath} | gzip > 1.filtlong_ont/${prefix}.${readstats}.fq.gz
+filtlong --min_length ${minsize} -t ${target} --length_weight ${weight} ${nanoporepath} | pigz -p ${threads} > 1.filtlong_ont/${prefix}.${readstats}.fq.gz
 
 
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