diff --git a/RQCP.sh b/RQCP.sh
index ff3d8889620a1f01dc4010aa9444d55ca6c5e460..2beb9f03c488950c82ef483a5babc8a3874f7c1d 100755
--- a/RQCP.sh
+++ b/RQCP.sh
@@ -56,7 +56,7 @@ echo "Quiet."
 echo "________________________________________________________________________"
 
 ###### Create dir for QC tools #####
-mkdir ${WORKDIR}/results/reads/cutadapt/ ${WORKDIR}/results/reads/sickle-trim/ ${WORKDIR}/results/reads/fastq-join/ 2> /dev/null
+mkdir ${WORKDIR}/results/reads/cutadapt/ ${WORKDIR}/results/reads/sickle-trim/ ${WORKDIR}/results/reads/fastq-join/ ${WORKDIR}/results/reads/merged/ 2> /dev/null
 
 ###### Extract bwa indexes for small genomes #####
 echo ""
diff --git a/config/config.yaml b/config/config.yaml
index cb2ec9286e17c01bcc0a24015abd3b4573107b48..db1a5479c2900bfd7e6bd6d6422d46a48ef0d912 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -35,6 +35,7 @@ datasets:
     #- 'sickle-single'
     - 'fastq-join'
     #- 'fastq-join-unique'
+    - 'merged'
   quality-tool:
     - 'fastqc'
     - 'fastq-screen'
diff --git a/resources/reads/.gitkeep b/resources/reads/.gitkeep
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/workflow/rules/reads_quality_control_pipeline.smk b/workflow/rules/reads_quality_control_pipeline.smk
index 559ff1a42d1f86f0e1f62b1fce9182816c1a9ac5..77afcc46e9f4ae3f02e380cec828c7404dcc6703 100644
--- a/workflow/rules/reads_quality_control_pipeline.smk
+++ b/workflow/rules/reads_quality_control_pipeline.smk
@@ -52,7 +52,7 @@ SUBSET = config["fastq-screen"]["subset"]   # Fastq-screen --subset
 ###############################################################################
 rule all:
     input:
-        joined = expand("results/reads/fastq-join/{sample}_cutadapt_sickle-trim_fastq-join_Mate.fastq.gz",
+        merged = expand("results/reads/merged/{sample}_cutadapt_sickle-trim_fastq-join_merged.fastq.gz",
                          sample = SAMPLE),
         multiqc = expand("results/quality/{qcdir}/multiqc/",
                          qcdir = QCDIR)
@@ -137,12 +137,33 @@ rule fastqc:
         "--outdir {output.fastqc} "   # -o: Create all output files in the specified output directory
         "{input.fastq}/*.fastq.gz "   # Input file.fastq
         "&> {log}"                    # Add redirection for log
-        
+
+###############################################################################
+rule merge:
+    # Aim: Merge all passing filters reads
+    # Use: cat {input} > {output}
+    priority: 1
+    message:
+        "Take all passing filter {wildcards.sample} reads"
+    input:
+        single = "results/reads/sickle-single/{sample}_cutadapt_sickle-trim_Single.fastq.gz",
+        forward= "results/reads/fastq-join-unique/{sample}_cutadapt_sickle-trim_fastq-join_Unique_R1.fastq.gz",
+        reverse = "results/reads/fastq-join-unique/{sample}_cutadapt_sickle-trim_fastq-join_Unique_R2.fastq.gz",
+        joined = "results/reads/fastq-join/{sample}_cutadapt_sickle-trim_fastq-join_Mate.fastq.gz",
+    output:
+        merged = "results/reads/merged/{sample}_cutadapt_sickle-trim_fastq-join_merged.fastq.gz"
+    shell:
+        "cat "              # Cat, concatenate
+        "{input.single} "   # Input trimmed singles fastq file from Sickle-trim 
+        "{input.forward} "  # Input unique forward files from Fastq-join
+        "{input.reverse} "  # Input unique reverse files from Fastq-join
+        "{input.joined} "   # Input join files from Fastq-join
+        "> {output.merged}" # Output merged
+     
 ###############################################################################
 rule fastqjoin:
     # Aim: joins two paired-end reads on the overlapping ends
     # Use: fastq-join [OPTIONS] <read1.fastq> <read2.fastq> [mate.fastq] -o <read.fastq> -o <read.fastq> -o <read.fastq>
-    priority: 1
     message:
         "Fastq-join assemble R1 and R2 from {wildcards.sample} reads"
     conda: