diff --git a/generation.sh b/generation.sh
index 07f7114..ac50caa 100755
--- a/generation.sh
+++ b/generation.sh
@@ -18,4 +18,5 @@ prefix="curesim_"
 
 Rscript src/repertoire.r "$sequences" "$number_of_reads" &&
 	java -jar tools/CuReSim.jar -f "$data_directory$filename$fastq" -o "$data_directory$prefix$filename$fastq"
+Rscript src/alignment.r
 rm "$data_directory/log.txt"