diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 9cb92df..0bb8c83 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -11,9 +11,13 @@ jobs:
   Formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+        with:
+          # super-linter needs the full git history to get the
+          # list of files that changed across commits
+          fetch-depth: 0
       - name: Formatting
-        uses: github/super-linter@v4
+        uses: github/super-linter@v7
         env:
           VALIDATE_ALL_CODEBASE: false
           DEFAULT_BRANCH: main
@@ -23,9 +27,9 @@ jobs:
   Linting:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
+      uses: snakemake/snakemake-github-action@v2
       with:
         directory: .
         snakefile: workflow/Snakefile
@@ -37,17 +41,17 @@ jobs:
       - Linting
       - Formatting
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Test workflow
-      uses: snakemake/snakemake-github-action@v1.24.0
+      uses: snakemake/snakemake-github-action@v2
       with:
         directory: .test
         snakefile: .test/Snakefile
         args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"
 
     - name: Test report
-      uses: snakemake/snakemake-github-action@v1.24.0
+      uses: snakemake/snakemake-github-action@v2
       with:
         directory: .test
         snakefile: .test/Snakefile
diff --git a/.test/config/config.yaml b/.test/config/config.yaml
index b469c8e..c1ebc86 100644
--- a/.test/config/config.yaml
+++ b/.test/config/config.yaml
@@ -9,13 +9,13 @@ ref:
   # Ensembl species name
   species: homo_sapiens
   # Ensembl release
-  release: 108
+  release: 113
   # Genome build
   build: GRCh38
   # Optionally, instead of downloading the whole reference from Ensembl via the 
   # parameters above, specify a specific chromosome below and uncomment the line.
   # This is usually only relevant for testing.
-  chromosome: 7
+  #chromosome: 7
 
 # These filters mostly correspond to the output columns of Circle-Map:
 # https://github.com/iprada/Circle-Map/wiki/Circle-Map-Realign-output-files
diff --git a/config/config.yaml b/config/config.yaml
index b36fded..f09b5c5 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -9,7 +9,7 @@ ref:
   # Ensembl species name
   species: homo_sapiens
   # Ensembl release
-  release: 108
+  release: 113
   # Genome build
   build: GRCh38
   # Optionally, instead of downloading the whole reference from Ensembl via the 
diff --git a/workflow/envs/annotatr.yaml b/workflow/envs/annotatr.yaml
new file mode 100644
index 0000000..937fba1
--- /dev/null
+++ b/workflow/envs/annotatr.yaml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bioconductor-annotatr =1.28
+  - r-tidyverse = 2.0
\ No newline at end of file
diff --git a/workflow/envs/biomart.yaml b/workflow/envs/biomart.yaml
new file mode 100644
index 0000000..b410e09
--- /dev/null
+++ b/workflow/envs/biomart.yaml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bioconductor-biomart =2.58
+  - r-tidyverse = 2.0
\ No newline at end of file
diff --git a/workflow/envs/rtracklayer.yaml b/workflow/envs/rtracklayer.yaml
new file mode 100644
index 0000000..f440c42
--- /dev/null
+++ b/workflow/envs/rtracklayer.yaml
@@ -0,0 +1,7 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bioconductor-rtracklayer =1.62
+  - r-tidyverse = 2.0
\ No newline at end of file
diff --git a/workflow/resources/circles.datavzrd.yaml b/workflow/resources/circles.datavzrd.yaml
index fb371fb..9be6e0a 100644
--- a/workflow/resources/circles.datavzrd.yaml
+++ b/workflow/resources/circles.datavzrd.yaml
@@ -1,15 +1,17 @@
+__use_yte__: true
+
 name: ?f"Extrachromosomal circular DNAs (eccDNAs) found by Circle-Map in sample '{wildcards.sample}'."
 
-default-view: circle_table
+default-view: circles_overview
 
 datasets:
-  circles:
-    path: ?input.circles
+  circles_overview:
+    path: ?input.circles_overview
     separator: "\t"
 
 views:
-  circle_table:
-    dataset: circles
+  circles_overview:
+    dataset: circles_overview
     page-size: 18
     desc: |
       ?"""
diff --git a/workflow/rules/circle_map.smk b/workflow/rules/circle_map.smk
index 057c23b..03c2709 100644
--- a/workflow/rules/circle_map.smk
+++ b/workflow/rules/circle_map.smk
@@ -76,3 +76,19 @@ rule clean_circle_map_realign_output:
         max_circle_length=config["circle_filtering"]["max_circle_length"],
     script:
         "../scripts/clean_circle_map_realign_output.py"
+
+
+rule annotate_cleaned_circles:
+    input:
+        all_annotations="resources/ensembl_all_annotations.harmonized.gff3.gz",
+        tsv="results/circle-map/{sample}.circles.cleaned.tsv",
+    output:
+        tsvs=directory("results/circle-map/{sample}.circles.cleaned.annotated/"),
+    log:
+        "logs/circle-map/{sample}.circles.cleaned.annotated.logs",
+    conda:
+        "../envs/annotatr.yaml"
+    params:
+        build=config["ref"]["build"],
+    script:
+        "../scripts/annotate_cleaned_circles.R"
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index ebf3165..4299360 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -83,6 +83,12 @@ def get_adapters(wildcards):
     ].get("adapters", ""),
 
 
+def get_bioc_species_name():
+    first_letter = config["ref"]["species"][0]
+    subspecies = config["ref"]["species"].split("_")[1]
+    return first_letter + subspecies
+
+
 def get_bwa_extra(wildcards):
     """
     Denote sample name and platform in read group.
diff --git a/workflow/rules/datavzrd.smk b/workflow/rules/datavzrd.smk
index 76deed3..65ad089 100644
--- a/workflow/rules/datavzrd.smk
+++ b/workflow/rules/datavzrd.smk
@@ -1,19 +1,8 @@
-rule render_datavzrd_config:
-    input:
-        template=workflow.source_path("../resources/circles.datavzrd.yaml"),
-        circles="results/circle-map/{sample}.circles.cleaned.tsv",
-    output:
-        "resources/datavzrd/circle-map/{sample}.circles.yaml",
-    log:
-        "logs/datavzrd/circle-map/{sample}.circles.rendering.log",
-    template_engine:
-        "yte"
-
-
 rule datavzrd:
     input:
-        config="resources/datavzrd/circle-map/{sample}.circles.yaml",
-        circles="results/circle-map/{sample}.circles.cleaned.tsv",
+        config=workflow.source_path("../resources/circles.datavzrd.yaml"),
+        circles_overview="results/circle-map/{sample}.circles.cleaned.tsv",
+        circles_tables="results/circle-map/{sample}.circles.cleaned.annotated/",
     output:
         report(
             directory("results/datavzrd/circles/{sample}"),
@@ -22,7 +11,8 @@ rule datavzrd:
             labels={"tool": "Circle-Map", "sample": "{sample}"},
             caption="../report/circle_map.rst",
         ),
+        config="resources/datavzrd/circle-map/{sample}.circles.datavzrd.rendered.yaml",
     log:
         "logs/datavzrd/circles/{sample}.log",
     wrapper:
-        "v3.8.0/utils/datavzrd"
+        "v7.0.0/utils/datavzrd"
diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 0958415..14e5454 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -10,6 +10,7 @@ rule get_genome:
         release=config["ref"]["release"],
         chromosome=config["ref"].get("chromosome"),
     cache: "omit-software"
+    localrule: True
     wrapper:
         "v1.21.2/bio/reference/ensembl-sequence"
 
@@ -69,6 +70,7 @@ rule get_known_variants:
         type="all",
         chromosome=config["ref"].get("chromosome"),
     cache: "omit-software"
+    localrule: True
     wrapper:
         "v1.21.2/bio/reference/ensembl-variation"
 
@@ -99,3 +101,105 @@ rule tabix_known_variants:
         "-p vcf",
     wrapper:
         "v1.21.2/bio/tabix/index"
+
+
+rule get_annotation:
+    output:
+        "resources/ensembl_genomic_annotations.gff3.gz",
+    params:
+        species=config["ref"]["species"],
+        release=config["ref"]["release"],
+        build=config["ref"]["build"],
+    log:
+        "logs/get-annotation.log",
+    cache: "omit-software"
+    localrule: True
+    wrapper:
+        "v3.13.6/bio/reference/ensembl-annotation"
+
+
+rule get_regulatory_features_gff3_gz:
+    output:
+        "resources/ensembl_regulatory_annotations.gff3.gz",  # presence of .gz determines if downloaded is kept compressed
+    params:
+        species=config["ref"]["species"],
+        release=config["ref"]["release"],
+        build=config["ref"]["build"],
+    log:
+        "logs/get_regulatory_features.log",
+    cache: "omit-software"  # save space and time with between workflow caching (see docs)
+    localrule: True
+    wrapper:
+        "v3.13.6/bio/reference/ensembl-regulation"
+
+
+rule get_repeat_features_tsv_gz:
+    output:
+        table="resources/ensembl_repeat_annotations.tsv.gz",  # .gz extension is optional, but recommended
+    params:
+        species=config["ref"]["species"],
+        release=config["ref"]["release"],
+        build=config["ref"]["build"],
+        main_tables={
+            "repeat_feature": {
+                "database": "core",
+            },
+        },
+        # choose the main table to retrieve, specifying { table : database }
+        join_tables={
+            "seq_region": {
+                "database": "core",
+                "join_column": "seq_region_id",
+            },
+            "repeat_consensus": {
+                "database": "core",
+                "join_column": "repeat_consensus_id",
+            },
+        },
+        # optional: add tables to join in for further annotations, specifying { table : { "database": database, "join_column": join-column } }
+    log:
+        "logs/create_repeat_annotations.log",
+    cache: "omit-software"  # save space and time with between workflow caching (see docs)
+    wrapper:
+        "v4.0.0/bio/reference/ensembl-mysql-table"
+
+
+rule create_transcripts_to_genes_mapping:
+    output:
+        table="resources/ensembl_transcripts_to_genes_mapping.tsv.gz",  # .gz extension is optional, but recommended
+    params:
+        biomart="genes",
+        species=config["ref"]["species"],
+        release=config["ref"]["release"],
+        build=config["ref"]["build"],
+        attributes=[
+            "ensembl_transcript_id",
+            "ensembl_gene_id",
+            "external_gene_name",
+            "genecards",
+        ],
+        #filters={ "chromosome_name": ["22", "X"] }, # optional: restrict output by using filters
+    log:
+        "logs/create_transcripts_to_genes_mapping.log",
+    cache: "omit-software"  # save space and time with between workflow caching (see docs)
+    wrapper:
+        "v4.0.0/bio/reference/ensembl-biomart-table"
+
+
+rule create_annotation_gff:
+    input:
+        genomic_annotations="resources/ensembl_genomic_annotations.gff3.gz",
+        mapping="resources/ensembl_transcripts_to_genes_mapping.tsv.gz",
+        regulatory_annotations="resources/ensembl_regulatory_annotations.gff3.gz",
+    output:
+        all_annotations="resources/ensembl_all_annotations.harmonized.gff3.gz",
+    log:
+        "logs/all_annotations.harmonized.gff3.log",
+    conda:
+        "../envs/rtracklayer.yaml"
+    params:
+        build=config["ref"]["build"],
+    resources:
+        mem_mb=lambda wc, input: 100 * input.size_mb,
+    script:
+        "../scripts/create_annotation_gff3.R"
diff --git a/workflow/scripts/annotate_cleaned_circles.R b/workflow/scripts/annotate_cleaned_circles.R
new file mode 100644
index 0000000..225efb3
--- /dev/null
+++ b/workflow/scripts/annotate_cleaned_circles.R
@@ -0,0 +1,117 @@
+log <- file(snakemake@log[[1]], open="wt")
+sink(log)
+sink(log, type="message")
+
+library("tidyverse")
+rlang::global_entrace()
+
+library("annotatr")
+library("GenomicRanges")
+
+circles <- read_tsv(
+  snakemake@input[["tsv"]]
+)
+
+genome_build <- snakemake@params[["build"]]
+
+circles_gr <- GRanges(
+  seqnames = pull(circles, region),
+  ecDNA_status = "ecDNA"
+)
+
+genome(circles_gr) <- genome_build
+
+overlapping_annotations <- rtracklayer::import(
+  snakemake@input[["all_annotations"]],
+  which = circles_gr, #import only intervals overlapping circles
+  genome = genome_build
+)
+
+dir.create(
+  snakemake@output[["tsvs"]],
+  recursive = TRUE
+)
+
+annotated_circles <- annotate_regions(
+  regions = circles_gr,
+  annotations = overlapping_annotations,
+  ignore.strand = TRUE,
+  quiet = FALSE
+) |>
+  as_tibble() |>
+  dplyr::select(
+    -c(
+      strand,
+      width,
+      ecDNA_status,
+      annot.width,
+      annot.source,
+      annot.score,
+      annot.phase
+    )
+  ) |>
+  arrange(
+    annot.seqnames,
+    annot.start,
+    annot.end
+  ) |>
+  mutate(
+    circle_region = str_c(
+      seqnames,
+      ":",
+      start,
+      "-",
+      end
+    ),
+    region = str_c(
+      annot.seqnames,
+      ":",
+      annot.start,
+      "-",
+      annot.end
+    )
+  ) |>
+  dplyr::select(
+    -c(
+      seqnames,
+      start,
+      end,
+      annot.seqnames,
+      annot.start,
+      annot.end
+    )
+  ) |>
+  dplyr::rename(
+    exon_rank = annot.rank
+  ) |>
+  dplyr::rename_with(
+    ~ str_replace(.x, fixed("annot."), "")
+  ) |>
+  dplyr::select(
+    region,
+    strand,
+    type,
+    ensembl_id,
+    name,
+    ensembl_transcript_id,
+    ensembl_gene_id,
+    hgnc_symbol,
+    genecards_id,
+    exon_rank,
+    circle_region,
+  ) |>
+  group_by(
+    circle_region
+  ) |>
+  group_walk(
+    ~ write_tsv(
+      .x,
+      file = file.path(
+        snakemake@output[["tsvs"]],
+        str_c(
+          str_replace_all(.y$circle_region, "[:-]", "_"),
+          ".tsv"
+        )
+      )
+    )
+  )
\ No newline at end of file
diff --git a/workflow/scripts/clean_circle_map_realign_output.py b/workflow/scripts/clean_circle_map_realign_output.py
index d76f1a1..9feb9c6 100644
--- a/workflow/scripts/clean_circle_map_realign_output.py
+++ b/workflow/scripts/clean_circle_map_realign_output.py
@@ -33,7 +33,7 @@
 ]
 
 # turn int cols into int
-circles.loc[:, int_cols] = circles.loc[:, int_cols].round(0).applymap(lambda v: int(v) if not pd.isna(v) else pd.NA)
+circles[int_cols] = circles[int_cols].round(0).map(lambda v: int(v) if not pd.isna(v) else pd.NA)
 
 # filter out low-quality circles, according to:
 # https://github.com/iprada/Circle-Map/wiki/Circle-Map-Realign-output-files
diff --git a/workflow/scripts/create_annotation_gff3.R b/workflow/scripts/create_annotation_gff3.R
new file mode 100644
index 0000000..0ae6f3d
--- /dev/null
+++ b/workflow/scripts/create_annotation_gff3.R
@@ -0,0 +1,196 @@
+log <- file(snakemake@log[[1]], open="wt")
+sink(log)
+sink(log, type="message")
+
+library("tidyverse")
+rlang::global_entrace()
+
+library("GenomicRanges")
+library("rtracklayer")
+
+transcripts_to_genes_mappings <- read_tsv(
+  snakemake@input[["mapping"]]
+)
+
+genome_build <- snakemake@params[["build"]]
+
+genomic_annotations <- rtracklayer::import(
+  snakemake@input[["genomic_annotations"]],
+  genome = genome_build,
+  feature.type = c(
+    "five_prime_UTR",
+    "three_prime_UTR",
+    "exon",
+    "gene",
+    "lnc_RNA",
+    "miRNA",
+    "snRNA",
+    "snoRNA",
+    "scRNA",
+    "rRNA",
+    "tRNA",
+    "V_gene_segment",
+    "D_gene_segment",
+    "J_gene_segment",
+    "C_gene_segment"
+  ),
+  colnames = c(
+    "type",
+    "Name",
+    "ID",
+    "Parent",
+    "rank",
+    "phase"
+  )
+) |>
+  as_tibble() |>
+  separate_wider_delim(
+    ID,
+    delim = ":",
+    names = c("id_type", "id")
+  ) |>
+  dplyr::select(-id_type) |>
+  unnest(
+    Parent,
+    keep_empty = TRUE
+  ) |>
+  separate_wider_delim(
+    Parent,
+    delim = ":",
+    names = c("parent_type", "parent_id")
+  ) |>
+  dplyr::rename(name = Name)
+
+regulatory_annotations <- rtracklayer::import(
+  snakemake@input[["regulatory_annotations"]],
+  genome = genome_build,
+  # make sure to expand parent_type generation below, if you add
+  # further types right here
+  feature.type = c(
+    "promoter",
+    "enhancer",
+    "TF_binding_site",
+    "CTCF_binding_site"
+  ),
+  colnames = c(
+    "type",
+    "ID",
+    "gene_id",
+    "gene_name",
+    "phase"
+  )
+) |>
+  as_tibble() |>
+  unnest_wider(
+    c(gene_id, gene_name),
+    names_sep = "-"
+  ) |> 
+  pivot_longer(
+    starts_with("gene_"),
+    names_to = c("id_type", "gene_nr"),
+    values_to = "val",
+    names_sep = "-"
+  ) |>
+  pivot_wider(
+    names_from = id_type,
+    values_from = val
+  ) |>
+  mutate(
+    gene_name = na_if(gene_name, "")
+  ) |>
+  filter(
+    !( gene_nr > 1 & is.na(gene_id) & is.na(gene_name) )
+  ) |>
+  dplyr::select(
+    !gene_nr
+  ) |>
+  dplyr::rename(
+    name = gene_name,
+    id = ID,
+    parent_id = gene_id,
+  ) |>
+  mutate(
+    rank = NA
+  )
+
+
+transcript_id_to_gene_id_mapping <- transcripts_to_genes_mappings |>
+  dplyr::select(
+    c(
+      ensembl_transcript_id,
+      ensembl_gene_id
+    )
+  ) |>
+  distinct()
+
+gene_id_annotations <- transcripts_to_genes_mappings |>
+  dplyr::select(
+    -ensembl_transcript_id
+  ) |>
+  distinct() |>
+  dplyr::rename(
+    hgnc_symbol = external_gene_name,
+    genecards_id = genecards
+  )
+
+all_annotations <- bind_rows(
+    genomic_annotations,
+    regulatory_annotations
+  ) |>
+  mutate(
+    ensembl_transcript_id = case_when(
+      str_detect(parent_id, "^ENST") ~ parent_id,
+      str_detect(id, "^ENST") ~ id
+    ),
+    gene_id = case_when(
+      str_detect(parent_id, "^ENSG") ~ parent_id,
+      str_detect(id, "^ENSG") ~ id,
+    )
+  ) |>
+  dplyr::select(
+    -c(
+      parent_type,
+      parent_id,
+      phase
+    )
+  ) |>
+  left_join(
+    transcript_id_to_gene_id_mapping,
+    by = join_by(
+      ensembl_transcript_id
+    )
+  ) |>
+  mutate(
+    ensembl_gene_id =  if_else(
+      is.na(ensembl_gene_id),
+      gene_id,
+      ensembl_gene_id
+    )
+  ) |>
+  dplyr::select(
+    -gene_id
+  ) |>
+  # bring in the gene symbols
+  left_join(
+    gene_id_annotations,
+    by = join_by(
+      ensembl_gene_id
+    )
+  ) |>
+  # make sure, everything has an `id`
+  mutate(
+    id = case_when(
+      is.na(id) & str_detect(name, "^ENS") ~ name,
+      is.na(id) & str_detect(type, "_UTR$") ~ ensembl_transcript_id,
+      .default = id
+    )
+  ) |>
+  dplyr::rename(
+    ensembl_id = id
+  ) |>
+  GRanges()
+
+seqlevels(all_annotations) <- sort(seqlevels(all_annotations))
+all_annotations <- sort(all_annotations, ignore.strand = TRUE)
+
+rtracklayer::export(all_annotations, snakemake@output[["all_annotations"]])
\ No newline at end of file