diff --git a/modules.json b/modules.json
index 926c7ad..2e3bc25 100644
--- a/modules.json
+++ b/modules.json
@@ -49,6 +49,11 @@
                         "branch": "master",
                         "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a",
                         "installed_by": ["modules"]
+                    },
+                    "seqtk/cutn": {
+                        "branch": "master",
+                        "git_sha": "7f88aae93c69586c0789322b77743ee0ef469502",
+                        "installed_by": ["modules"]
                     }
                 }
             },
diff --git a/modules/nf-core/seqtk/cutn/environment.yml b/modules/nf-core/seqtk/cutn/environment.yml
new file mode 100644
index 0000000..a57afbb
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/environment.yml
@@ -0,0 +1,7 @@
+name: seqtk_cutn
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::seqtk=1.4
diff --git a/modules/nf-core/seqtk/cutn/main.nf b/modules/nf-core/seqtk/cutn/main.nf
new file mode 100644
index 0000000..c2344a8
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/main.nf
@@ -0,0 +1,49 @@
+process SEQTK_CUTN {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_1' :
+        'biocontainers/seqtk:1.4--he4a0461_1' }"
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.bed")    , emit: bed
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    seqtk \\
+        cutN \\
+        $args \\
+        -g $fasta \\
+        > ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+}
diff --git a/modules/nf-core/seqtk/cutn/meta.yml b/modules/nf-core/seqtk/cutn/meta.yml
new file mode 100644
index 0000000..1082867
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/meta.yml
@@ -0,0 +1,41 @@
+name: seqtk_cutn
+description: Generates a BED file containing genomic locations of lengths of N.
+keywords:
+  - cut
+  - fasta
+  - seqtk
+tools:
+  - seqtk:
+      description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file.
+      homepage: https://github.com/lh3/seqtk
+      documentation: https://docs.csc.fi/apps/seqtk/
+      tool_dev_url: https://github.com/lh3/seqtk
+      licence: ["MIT"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: A single fasta file to be split.
+      pattern: "*.{fasta}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: The output bed which summarised locations of cuts
+      pattern: "*.{bed}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+authors:
+  - "@DLBPointon"
+maintainers:
+  - "@DLBPointon"
diff --git a/modules/nf-core/seqtk/cutn/tests/main.nf.test b/modules/nf-core/seqtk/cutn/tests/main.nf.test
new file mode 100644
index 0000000..a38ed41
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/tests/main.nf.test
@@ -0,0 +1,57 @@
+nextflow_process {
+
+    name "Test Process SEQTK_CUTN"
+    script "../main.nf"
+    process "SEQTK_CUTN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqtk"
+    tag "seqtk/cutn"
+
+    test("homo_21_cut") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:true ],
+                                file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() },
+                { assert snapshot(
+                            file(process.out.bed[0][1]).name
+                                ).match("genome_cut")
+                }
+            )
+        }
+    }
+
+    test("homo_21_cut_stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                                [ id:'test', single_end:true ],
+                                file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/seqtk/cutn/tests/main.nf.test.snap b/modules/nf-core/seqtk/cutn/tests/main.nf.test.snap
new file mode 100644
index 0000000..998beda
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/tests/main.nf.test.snap
@@ -0,0 +1,70 @@
+{
+    "genome_cut": {
+        "content": [
+            "test.bed"
+        ],
+        "timestamp": "2024-02-22T16:02:14.744148"
+    },
+    "homo_21_cut_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3da8ed2738f3c093d1e62d796fd76428"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3da8ed2738f3c093d1e62d796fd76428"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-22T16:02:23.596389"
+    },
+    "homo_21_cut": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed:md5,16cbba84e3a4bdbb52217afb5051f948"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,3da8ed2738f3c093d1e62d796fd76428"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.bed:md5,16cbba84e3a4bdbb52217afb5051f948"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,3da8ed2738f3c093d1e62d796fd76428"
+                ]
+            }
+        ],
+        "timestamp": "2024-02-22T16:02:14.695205"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/seqtk/cutn/tests/tags.yml b/modules/nf-core/seqtk/cutn/tests/tags.yml
new file mode 100644
index 0000000..13c64cc
--- /dev/null
+++ b/modules/nf-core/seqtk/cutn/tests/tags.yml
@@ -0,0 +1,2 @@
+seqtk/cutn:
+  - "modules/nf-core/seqtk/cutn/**"
diff --git a/workflows/pairgenomealign.nf b/workflows/pairgenomealign.nf
index e1f6eda..bc76f6a 100644
--- a/workflows/pairgenomealign.nf
+++ b/workflows/pairgenomealign.nf
@@ -6,6 +6,8 @@
 
 include { ASSEMBLYSCAN           } from '../modules/nf-core/assemblyscan/main'
 include { PAIRALIGN_M2M          } from '../subworkflows/local/pairalign_m2m/main'
+include { SEQTK_CUTN as SEQTK_CUTN_TARGET  } from '../modules/nf-core/seqtk/cutn/main'
+include { SEQTK_CUTN as SEQTK_CUTN_QUERY  } from '../modules/nf-core/seqtk/cutn/main'
 include { PAIRALIGN_M2O          } from '../subworkflows/local/pairalign_m2o/main'
 include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-validation'
@@ -30,6 +32,20 @@ workflow PAIRGENOMEALIGN {
     ch_versions = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
+    //
+    // MODULE: seqtk_cutn_target
+    //
+    SEQTK_CUTN_TARGET (
+        ch_targetgenome
+    )
+
+    //
+    // MODULE: seqtk_cutn_query
+    //
+    SEQTK_CUTN_QUERY (
+        ch_samplesheet
+    )
+
     //
     // MODULE: assembly-scan
     //