diff --git a/src/tirmite/bowtie2_wrappers.py b/src/tirmite/bowtie2_wrappers.py
deleted file mode 100644
index 005691e..0000000
--- a/src/tirmite/bowtie2_wrappers.py
+++ /dev/null
@@ -1,68 +0,0 @@
-import os
-from shlex import quote
-
-
-def _bowtie2build_cmd(bt2Path="bowtie2-build", IdxPath="db/GenIdx", genome=None):
-    """Construct the bowtie2-build command"""
-    # Base command
-    cmd = " ".join(
-        ["mkdir db &&", quote(bt2Path), quote(os.path.abspath(genome)), IdxPath]
-    )
-    return cmd
-
-
-def _bowtie2_cmd(bt2Path="bowtie2", tirFasta=None, IdxPath="db/GenIdx", cores=None):
-    """Construct commands for bowtie2 mapping."""
-    # bowtie2 -x genidx -f -a --very-sensitive-local -U TIR.fa --al alignments.bam
-    # Base command
-    cmd = " ".join(
-        [
-            quote(bt2Path),
-            "-f -a --very-sensitive-local -x",
-            IdxPath,
-            "-U",
-            quote(os.path.abspath(tirFasta)),
-            "> alignments.sam",
-        ]
-    )
-    # Optional set cores
-    if cores:
-        cmd += " --threads " + str(cores)
-    return cmd
-
-
-def _bam2bed_cmd(samPath="samtools", bedPath="bedtools", tempDir=None):
-    """Filtering mapped reads with bedtools and samtools.
-    # Fwd hits
-    samtools view -b -F 0x10 alignments.sam | bedtools bamtobed -i stdin | awk -v OFS='\t' '{print $1,$2,$3,"+"}' > mapped.bed
-    # Rev hits
-    samtools view -b -f 0x10 alignments.sam | bedtools bamtobed -i stdin | awk -v OFS='\t' '{print $1,$2,$3,"-"}' >> mapped.bed
-    """
-    # Base command
-    mappedPath = os.path.join(tempDir, "bowtie2mappedTIR.bed")
-    cmds = list()
-    # All reads not on rev strand or unmapped
-    cmds.append(
-        " ".join(
-            [
-                quote(samPath),
-                "view -b -F 0x10,0x4 alignments.sam |",
-                quote(bedPath),
-                "bamtobed -i stdin | awk -v OFS='\\t' '{print $1,$2,$3,\"+\"}' >",
-                quote(mappedPath),
-            ]
-        )
-    )
-    # Only reads on reverse strand
-    cmds.append(
-        " ".join(
-            [
-                quote(samPath),
-                "view -b -f 0x10 alignments.sam |",
-                quote(bedPath),
-                "bamtobed -i stdin | awk -v OFS='\\t' '{print $1,$2,$3,\"-\"}' >>",
-                quote(mappedPath),
-            ]
-        )
-    )
-    return cmds, mappedPath