diff --git a/genpipes/bfx/kallisto.py b/genpipes/bfx/kallisto.py
index a2d865a39..a679e4e3b 100644
--- a/genpipes/bfx/kallisto.py
+++ b/genpipes/bfx/kallisto.py
@@ -29,7 +29,8 @@ def quant(
     inputs,
     output_dir,
     transcriptome,
-    parameters
+    parameters,
+    ini_section="kallisto"
     ):
     """
     Call to kalliso quant
@@ -43,18 +44,19 @@ def quant(
             os.path.join(output_dir, "abundance.h5")
             ],
         [
-            ['kallisto', 'module_kallisto']
+            [ini_section, 'module_kallisto']
         ],
         command="""\
-kallisto quant \\
+kallisto quant {other_options} \\
   {parameters} \\
   -t {threads} \\
   -i {transcriptome} \\
   -o {output_dir} \\
   {infiles} \\
   2> {output_dir}/kallisto_quant.log""".format(
+            other_options=global_conf.global_get(ini_section, 'other_options'),
             parameters=parameters,
-            threads=global_conf.global_get('kallisto', 'threads'),
+            threads=global_conf.global_get(ini_section, 'threads'),
             transcriptome=transcriptome,
             output_dir=output_dir,
             infiles=" \\\n  ".join(inputs),
diff --git a/genpipes/pipelines/rnaseq_light/rnaseq_light.base.ini b/genpipes/pipelines/rnaseq_light/rnaseq_light.base.ini
index 9b5e34ab8..8fd9c4187 100755
--- a/genpipes/pipelines/rnaseq_light/rnaseq_light.base.ini
+++ b/genpipes/pipelines/rnaseq_light/rnaseq_light.base.ini
@@ -94,6 +94,7 @@ java_other_options = -XX:ParallelGCThreads=5 -Dsamjdk.buffer_size=1048576
 
 [kallisto]
 module_R=mugqic/R_Bioconductor/3.5.0_3.7
+other_options=
 # note that kallisto indexes on cvmfs should contain the name of the kallisto version. Any versions without this naming structure are retained on cvmfs only for legacy reasons
 transcriptome_idx = %(annotation_dir)s/cdna_kallisto_index/%(scientific_name)s.%(assembly)s.%(source)s%(version)s.kallisto-%(kallisto_version)s.cdna.fa.idx
 transcript2genes = %(annotation_dir)s/cdna_kallisto_index/%(scientific_name)s.%(assembly)s.%(source)s%(version)s.tx2gene