diff --git a/Snakefile b/Snakefile
index 2f5842ad042cb5bd14cb17afb3d72795efff88fc..f0303c37dce4746277e1740889cddecba227601a 100644
--- a/Snakefile
+++ b/Snakefile
@@ -302,7 +302,7 @@ rule create_index_star:
             )
 
     singularity:
-        "docker://zavolab/star:2.7.3a-slim"
+        "docker://quay.io/biocontainers/star:2.7.3a--0"
 
     threads: 12
 
@@ -371,7 +371,7 @@ rule extract_transcriptome:
             current_rule + "_{organism}.log")
 
     singularity:
-        "docker://zavolab/gffread:0.11.7-slim"
+        "docker://quay.io/biocontainers/gffread:0.11.7--h8b12597_0"
 
     shell:
         "(gffread \
@@ -462,7 +462,7 @@ rule create_index_salmon:
             )
 
     singularity:
-        "docker://zavolab/salmon:1.1.0-slim"
+        "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
 
     log:
         stderr = os.path.join(
@@ -516,7 +516,7 @@ rule create_index_kallisto:
             )
 
     singularity:
-        "docker://zavolab/kallisto:0.46.1-slim"
+        "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
 
     log:
         stderr = os.path.join(
@@ -609,7 +609,7 @@ rule index_genomic_alignment_samtools:
             )
 
     singularity:
-        "docker://zavolab/samtools:1.10-slim"
+        "docker://quay.io/biocontainers/samtools:1.10--h2e538c0_3"
 
     threads: 1
 
@@ -779,7 +779,7 @@ rule salmon_quantmerge_genes:
     threads: 1
 
     singularity:
-        "docker://zavolab/salmon:1.1.0-slim"
+        "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
 
     shell:
         "(salmon quantmerge \
@@ -862,7 +862,7 @@ rule salmon_quantmerge_transcripts:
     threads: 1
 
     singularity:
-        "docker://zavolab/salmon:1.1.0-slim"
+        "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
 
     shell:
         "(salmon quantmerge \
@@ -1208,7 +1208,7 @@ rule star_rpm:
             )
 
     singularity:
-        "docker://zavolab/star:2.7.3a-slim"
+        "docker://quay.io/biocontainers/star:2.7.3a--0"
 
     log:
         stderr = os.path.join(
@@ -1674,7 +1674,7 @@ rule sort_bed_4_big:
             )
 
     singularity:
-        "docker://cjh4zavolab/bedtools:2.27"
+        "docker://quay.io/biocontainers/bedtools:2.27.1--h9a82719_5"
 
     log:
         stderr = os.path.join(
@@ -1734,7 +1734,7 @@ rule prepare_bigWig:
             )
 
     singularity:
-        "docker://zavolab/bedgraphtobigwig:4-slim"
+        "docker://quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h0b8a92a_2"
 
     log:
         stderr = os.path.join(
diff --git a/workflow/rules/paired_end.snakefile.smk b/workflow/rules/paired_end.snakefile.smk
index 3f7834cb49f85437ad83fade6cf66b91e2b682ec..78d9937131af38f3a08ad1ee317e955ce176c1d0 100644
--- a/workflow/rules/paired_end.snakefile.smk
+++ b/workflow/rules/paired_end.snakefile.smk
@@ -53,7 +53,7 @@ rule pe_remove_adapters_cutadapt:
             )
 
     singularity:
-        "docker://zavolab/cutadapt:1.16-slim"
+        "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
 
     threads: 8
 
@@ -148,7 +148,7 @@ rule pe_remove_polya_cutadapt:
             )
 
     singularity:
-        "docker://zavolab/cutadapt:1.16-slim"
+        "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
 
     threads: 8
 
@@ -279,7 +279,7 @@ rule pe_map_genome_star:
             )
 
     singularity:
-        "docker://zavolab/star:2.7.3a-slim"
+        "docker://quay.io/biocontainers/star:2.7.3a--0"
 
     threads: 12
 
@@ -414,7 +414,7 @@ rule pe_quantification_salmon:
     threads: 6
 
     singularity:
-        "docker://zavolab/salmon:1.1.0-slim"
+        "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
 
     shell:
         "(salmon quant \
@@ -498,7 +498,7 @@ rule pe_genome_quantification_kallisto:
 
 
     singularity:
-        "docker://zavolab/kallisto:0.46.1-slim"
+        "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
 
     threads: 8
 
diff --git a/workflow/rules/single_end.snakefile.smk b/workflow/rules/single_end.snakefile.smk
index 337ae752b58ddaccdfcd351b63e6cc18b2982934..ae6e01bd189180f9bcd613ab49f891cdce227216 100644
--- a/workflow/rules/single_end.snakefile.smk
+++ b/workflow/rules/single_end.snakefile.smk
@@ -43,7 +43,7 @@ rule remove_adapters_cutadapt:
             )
 
     singularity:
-        "docker://zavolab/cutadapt:1.16-slim"
+        "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
 
     threads: 8
 
@@ -113,7 +113,7 @@ rule remove_polya_cutadapt:
             )
 
     singularity:
-        "docker://zavolab/cutadapt:1.16-slim"
+        "docker://quay.io/biocontainers/cutadapt:1.16--py35_2"
 
     threads: 8
 
@@ -223,7 +223,7 @@ rule map_genome_star:
             )
 
     singularity:
-        "docker://zavolab/star:2.7.3a-slim"
+        "docker://quay.io/biocontainers/star:2.7.3a--0"
 
     threads: 12
 
@@ -361,7 +361,7 @@ rule quantification_salmon:
     threads: 12
 
     singularity:
-        "docker://zavolab/salmon:1.1.0-slim"
+        "docker://quay.io/biocontainers/salmon:1.1.0--hf69c8f4_0"
 
     shell:
         "(salmon quant \
@@ -459,7 +459,7 @@ rule genome_quantification_kallisto:
             current_rule + ".se.stderr.log")
 
     singularity:
-        "docker://zavolab/kallisto:0.46.1-slim"
+        "docker://quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0"
 
     shell:
         "(kallisto quant \