diff --git a/data/sample_mbelari.csv b/data/sample_mbelari.csv
index 398a4b4c996b8b609d0f23599b9d2ff7ab4e5b87..76e8c0cdf110d2af7a476f34dc1e9805e9dc5135 100644
--- a/data/sample_mbelari.csv
+++ b/data/sample_mbelari.csv
@@ -1,9 +1,9 @@
-female1: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fastq
-female2: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fastq
-female3: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fastq
-female4: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fastq
-female5: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fastq
-female6: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fastq
-female7: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fastq
-male1: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fastq ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fastq
-male2: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fastq ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fastq
+female1: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fastq.gz
+female2: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fastq.gz
+female3: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fastq.gz
+female4: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fastq.gz
+female5: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fastq.gz
+female6: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fastq.gz
+female7: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fastq.gz
+male1: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fastq.gz
+male2: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fastq.gz
diff --git a/data/sample_mlongespiculosa.csv b/data/sample_mlongespiculosa.csv
index 8217973f3914568090756f258d6548896df79b7d..9c05514ee12f2730eb31dc61df0631f5f2fc3a71 100644
--- a/data/sample_mlongespiculosa.csv
+++ b/data/sample_mlongespiculosa.csv
@@ -1,2 +1,2 @@
-female1: /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fastq
-male1: //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq ; //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq
+female1: /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fastq.gz
+male1: //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq.gz
diff --git a/data/sample_mspiculigera.csv b/data/sample_mspiculigera.csv
index d58b9451a49138a9c38e662755045412f2f65bd8..534ec50636a7c973d2a339dbc03f4131907ab655 100644
--- a/data/sample_mspiculigera.csv
+++ b/data/sample_mspiculigera.csv
@@ -1,2 +1,2 @@
-female1: /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fastq ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fastq
-male1: //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fastq ; //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fastq
+female1: /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fastq.gz
+male1: //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fastq.gz