diff --git a/bio/samtools/fastq/separate/test/Snakefile b/bio/samtools/fastq/separate/test/Snakefile
index eb899a1a95..7c8a38be41 100644
--- a/bio/samtools/fastq/separate/test/Snakefile
+++ b/bio/samtools/fastq/separate/test/Snakefile
@@ -7,7 +7,7 @@ rule samtools_fastq_separate:
     log:
         "{sample}.separate.log",
     params:
-        sort="-m 4G",
+        collate="",
         fastq="-n",
     # Remember, this is the number of samtools' additional threads. At least 2 threads have to be requested on cluster sumbission. This value - 2 will be sent to samtools sort -@ argument.
     threads: 3
diff --git a/bio/samtools/fastq/separate/wrapper.py b/bio/samtools/fastq/separate/wrapper.py
index d4f8d1b0ff..581a192099 100644
--- a/bio/samtools/fastq/separate/wrapper.py
+++ b/bio/samtools/fastq/separate/wrapper.py
@@ -10,37 +10,29 @@
 from snakemake.shell import shell
 from snakemake_wrapper_utils.snakemake import get_mem
 
-params_sort = snakemake.params.get("sort", "")
+params_collate = snakemake.params.get("collate", "")
 params_fastq = snakemake.params.get("fastq", "")
 log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
 # Samtools takes additional threads through its option -@
-# One thread is used bu Samtools sort
+# One thread is used by Samtools collate
 # One thread is used by Samtools fastq
 # So snakemake.threads has to take them into account
 # before allowing additional threads through samtools sort -@
 threads = 0 if snakemake.threads <= 2 else snakemake.threads - 2
 
-mem = get_mem(snakemake, "MiB")
-mem = "-m {0:.0f}M".format(mem / threads) if mem and threads else ""
-
-with tempfile.TemporaryDirectory() as tmpdir:
-    tmp_prefix = Path(tmpdir) / "samtools_fastq.sort"
-
-    shell(
-        "(samtools sort -n"
-        " --threads {threads}"
-        " {mem}"
-        " -T {tmp_prefix}"
-        " {params_sort}"
-        " {snakemake.input[0]} | "
-        "samtools fastq"
-        " {params_fastq}"
-        " -1 {snakemake.output[0]}"
-        " -2 {snakemake.output[1]}"
-        " -0 /dev/null"
-        " -s /dev/null"
-        " -F 0x900"
-        " - "
-        ") {log}"
-    )
+shell(
+    "(samtools collate -u -O"
+    " --threads {threads}"
+    " {params_collate}"
+    " {snakemake.input[0]} | "
+    "samtools fastq"
+    " {params_fastq}"
+    " -1 {snakemake.output[0]}"
+    " -2 {snakemake.output[1]}"
+    " -0 /dev/null"
+    " -s /dev/null"
+    " -F 0x900"
+    " - "
+    ") {log}"
+)