diff --git a/filterAndTrim.R b/filterAndTrim.R
new file mode 100644
index 0000000000000000000000000000000000000000..c1ab729adb04d34be0fb472afb998cb3ca9ff44a
--- /dev/null
+++ b/filterAndTrim.R
@@ -0,0 +1,3 @@
+library(dada2)
+
+filterAndTrim(snakemake@input[[1]], snakemake@output[[1]], maxN=0, rm.phix=TRUE, compress=TRUE, verbose = TRUE)
diff --git a/preprocess.smk b/preprocess.smk
index d5f8f3f62204d3e644d79f924ff2a79dbb3c4e09..56b94b62801d29baabc111108cc1067f1a74fe70 100644
--- a/preprocess.smk
+++ b/preprocess.smk
@@ -15,3 +15,11 @@ rule cutadapt:
         "--match-read-wildcards " 
         "-o {output} " 
         "{input} "
+
+rule filter:
+	input:
+		"work/cutadapt/{sample}.fastq.gz"
+	output:
+		"work/filter/{sample}.fastq.gz"
+	script:
+		"filterAndTrim.R"