diff --git a/tools/flye/flye.rule.snakefile b/tools/flye/flye.rule.snakefile
new file mode 100755
index 0000000000000000000000000000000000000000..d57d5538bf2b1aa76f7f17b309c458f57fa5d3bc
--- /dev/null
+++ b/tools/flye/flye.rule.snakefile
@@ -0,0 +1,24 @@
+rule <step_name>__flye:
+    input:
+        **<step_name>__flye_inputs(),
+    output: 
+        assembly_fasta = config["results_dir"] + "/" + config["<step_name>__flye_output_dir"] + "/assembly.fasta",
+        assembly_info = config["results_dir"] + "/" + config["<step_name>__flye_output_dir"] + "/assembly.info",
+    params:
+        command = config["<step_name>__flye_command"],
+        output_dir = config["results_dir"] + "/" + config["<step_name>__flye_output_dir"]+ "/",
+        pacbio_oxfordNanopore = config["<step_name>__flye_pacbio_oxfordNanopore"],
+        scaffold = "--scaffold" if config["<step_name>__flye_scaffold"], else "", 
+        keep_haplotypes = "--keep-haplotypes" if config["<step_name>__flye_keep_haplotypes"] else "",
+    log: 
+        config["results_dir"] + "/logs/" + config["<step_name>__flye_output_dir"] + "/flye_log.txt"
+    threads: 
+        config["<step_name>__flye_threads"]
+    shell: 
+        "{params.command} {params.pacbio_oxfordNanopore} "
+        "{input.read} "
+        "--out-dir {params.output_dir} "
+        "-t {threads} "
+        "{params.scaffold} {params.keep_haplotypes} |& tee {log} ;"
+        "awk '/^>/ {{printf(\"\n%s\n\",$0);next; }} {{ printf(\"%s\",$0);}}  END {{printf(\"\n\");}}' < {params.output_dir}/assembly.fasta > {params.output_dir}/assembly.fa; "
+        "mv {params.output_dir}/assembly.fa > {params.output_dir}/assembly.fasta"
\ No newline at end of file
diff --git a/tools/flye/flye.yaml b/tools/flye/flye.yaml
new file mode 100755
index 0000000000000000000000000000000000000000..382749b3771ffeb307d51ba638a72dbde4e9e0aa
--- /dev/null
+++ b/tools/flye/flye.yaml
@@ -0,0 +1,82 @@
+{
+  id: flye,
+  name: flye,
+  article: "s41592-020-00971-x",
+  website: "https://github.com/fenderglass/Flye/blob/flye/docs/FAQ.md",
+  git: "https://github.com/fenderglass/Flye",
+  description: "Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.",
+  version: "2.9",
+  documentation: "https://github.com/fenderglass/Flye/tree/flye/docs",
+  multiqc: "custom",
+  commands:
+    [
+      {
+        name: flye,
+        cname: "Flye assembler",
+        command:  flye,
+        category: "assembly",
+        output_dir: flye,
+        inputs: [{ name: read, type: "reads" }],
+        outputs:
+        [
+          { name: assembly_info, type: "tsv", file: assembly_info.txt , description: "Extra information about contigs" },
+          { name: assembly_fasta, type: "fasta", file: assembly.fasta, description: "Final assembly. Contains contigs and possibly scaffolds" }
+        ],
+        options:
+          [
+            {
+              name: flye_threads,
+              prefix: -t,
+              type: numeric,
+              value: 4,
+              min: 1,
+              max: NA,
+              step: 1,
+              label: "Number of threads to use",
+            },
+            {
+              name: "flye_pacbio_oxfordNanopore",
+              type: "select",
+              value: "--nano-hq",
+              choices: [
+                Pacbio raw: --pacbio-raw,
+                Pacbio corre: --pacbio-corr,
+                Pacbio hifi: --pacbio-hifi,
+                ONT raw: --nano-raw,
+                ONT corr: --nano-corr,
+                ONT hq: '--nano-hq'
+                ],
+              label: "Reads type",
+            },
+            {
+            name: flye_keep_haplotype,
+            prefix: "--keep-haplotypes",
+            type: checkbox,
+            value: False,
+            label: "do not collapse alternative haplotypes",
+            },
+            {
+            name: flye_scaffold,
+            prefix: "--scaffold",
+            type: checkbox,
+            value: False,
+            label: "enable scaffolding using graph",
+            },
+          ],
+      },
+    ],
+  install: {
+    minimap2: [
+      "cd /opt/biotools",
+      "git clone https://github.com/fenderglass/Flye",
+      "cd Flye",
+      "make",
+      "ENV PATH /opt/biotools/Flye/bin:$PATH"
+    ]
+  },
+  citations:  {
+    minimap2: [
+      "Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner metaFlye: scalable long-read metagenome assembly using repeat graphs", Nature Methods, 2020"
+    ]
+  }
+}
\ No newline at end of file