diff --git a/.github/workflows/clippy.yml b/.github/workflows/clippy.yml
new file mode 100644
index 0000000..03b0edd
--- /dev/null
+++ b/.github/workflows/clippy.yml
@@ -0,0 +1,48 @@
+# Clippy is a tool that runs a bunch of tests on the Rust code to catch common mistakes and discouraged patterns.
+
+name: Analyze with Rust Clippy
+
+on:
+  push:
+    branches: 
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+
+jobs:
+  rust-clippy-analyze:
+    name: Run rust-clippy analyzing
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      security-events: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install Rust toolchain
+        uses: actions-rs/toolchain@16499b5e05bf2e26879000db0c1d13f7e13fa3af #@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          components: clippy
+          override: true
+
+      - name: Install required cargo
+        run: cargo install clippy-sarif sarif-fmt
+
+      - name: Run rust-clippy
+        run:
+          cargo clippy
+          --all-features
+          --message-format=json | clippy-sarif | tee rust-clippy-results.sarif | sarif-fmt
+        continue-on-error: true
+
+      - name: Upload analysis results to GitHub
+        uses: github/codeql-action/upload-sarif@v1
+        with:
+          sarif_file: rust-clippy-results.sarif
+          wait-for-processing: true
\ No newline at end of file
diff --git a/.github/workflows/dockerhub.yml b/.github/workflows/dockerhub.yml
new file mode 100644
index 0000000..064e2ce
--- /dev/null
+++ b/.github/workflows/dockerhub.yml
@@ -0,0 +1,60 @@
+name: Publish to Dockerhub
+
+on:
+  push:
+    branches:
+      - main
+      - 'releases/**'
+      - AddCIpipelines
+    tags:
+      - 'v*' #if a push with a version tag like v0.0.2 is recorded
+
+  release:
+    types: [published]
+
+jobs:
+  push_to_registry:
+    if: github.repository == 'SciLifeLab/umi-transfer'
+    name: Push Docker image to Docker Hub / GitHub Docker Registry
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v2
+
+      - name: Change repo name to lowercase
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >>${GITHUB_ENV}
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: ${{ github.repository_owner }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Push dev image
+        uses: docker/build-push-action@v2
+        if: github.event_name == 'push'
+        with:
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:dev
+            ghcr.io/${{ env.REPO_LOWERCASE }}:dev
+            
+      - name: Push release image
+        uses: docker/build-push-action@v2
+        if: github.event_name == 'release'
+        with:
+          push: true
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:${{ github.event.release.tag_name }}
+            ${{ secrets.DOCKERHUB_USERNAME }}/umi-transfer:latest
+            ghcr.io/${{ env.REPO_LOWERCASE }}:${{ github.event.release.tag_name }}
+            ghcr.io/${{ env.REPO_LOWERCASE }}:${{ github.sha }}
+            ghcr.io/${{ env.REPO_LOWERCASE }}:latest
diff --git a/.github/workflows/rust.yml b/.github/workflows/rust.yml
new file mode 100644
index 0000000..d79b62c
--- /dev/null
+++ b/.github/workflows/rust.yml
@@ -0,0 +1,21 @@
+name: Test successful compilation on Rust
+
+on: [push]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Rust
+      uses: actions-rs/toolchain@v1
+      with:
+          toolchain: stable
+          override: true
+          target: wasm32-unknown-unknown
+    - name: Build
+      uses: actions-rs/cargo@v1
+      with:
+        command: build
diff --git a/Cargo.lock b/Cargo.lock
new file mode 100644
index 0000000..703d3d0
--- /dev/null
+++ b/Cargo.lock
@@ -0,0 +1,898 @@
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diff --git a/Cargo.toml b/Cargo.toml
new file mode 100644
index 0000000..db354c6
--- /dev/null
+++ b/Cargo.toml
@@ -0,0 +1,12 @@
+[package]
+name = "umi-transfer"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+clap = { version = "3.2.10", features = ["derive"] }
+bio = "0.41.0"
+regex = "1.6.0"
+lazy_static = "1.4"
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..4d1e92f
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,18 @@
+FROM rust:latest as buildenv
+
+WORKDIR /usr/app/src
+COPY ./ /usr/app/src
+
+RUN apt-get update && apt-get -y install clang cmake && \
+    rm -rf /var/lib/apt/lists/* && \
+    rustup component add rustfmt 
+
+RUN --mount=type=cache,target=/usr/local/cargo/registry \
+    --mount=type=cache,target=/rust/target \
+    cargo build --release
+
+FROM debian:bullseye-slim as runner
+WORKDIR /root
+COPY --from=buildenv /usr/app/src/target/release/ /usr/local/bin/
+RUN chmod +x /usr/local/bin/umi-transfer
+CMD /usr/local/bin/umi-transfer
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..66df55b
--- /dev/null
+++ b/README.md
@@ -0,0 +1,44 @@
+# Building
+
+Go to the directory with the tool and type in `cargo build` .
+
+# Running
+
+### Usage
+
+The tool requires an input as follows:
+
+> `umi-transfer [OPTIONS] <SUBCOMMAND> `<br>
+
+`OPTIONS:`
+| Flag | Required | Description |
+| ------------- | :-----------: | ----------: |
+| `-h`,`--help` | No | Print help information |
+| `--prefix` | No, but default will be '`integrated`' | dictates name of output files|
+| `--r1-in` | Yes | FASTQ file with reads|
+| `--r2-in` | No | FASTQ file with reads |
+
+`SUBCOMMANDS: `
+
+> `inline:`
+>
+> > | Flag         |          Required          |                Description |
+> > | ------------ | :------------------------: | -------------------------: |
+> > | `--pattern1` |            Yes             | Nucleotide Pattern for UMI |
+> > | `--pattern2` | Needed if `--r2-in` exists | Nucleotide Pattern for UMI |
+>
+> `separate:`
+>
+> > | Flag      | Required |                  Description |
+> > | --------- | :------: | ---------------------------: |
+> > | `--ru-in` |   Yes    | FASTQ containing UMI records |
+
+Running the tool can be done by `cargo run --release -- [options] --r1-in 'fastq' <Subcommands> `, where the `--release` flag is optional, but will ensure an optimized build. <br>
+
+### Inline UMI extraction example:
+
+`cargo run --release -- --prefix 'output' --r1-in 'R1.fastq' --r2-in 'R2.fastq' inline --pattern1 'NNNNNNNNN' --pattern2 'NNNNNNNNN'`
+
+### UMI in seperate file example:
+
+`cargo run --release -- --prefix 'output' --r1-in 'R1.fastq' --r2-in 'R3.fastq' separate --ru-in 'R2.fastq'`
diff --git a/src/main.rs b/src/main.rs
new file mode 100644
index 0000000..9c55991
--- /dev/null
+++ b/src/main.rs
@@ -0,0 +1,192 @@
+use clap::Parser;
+use std::iter::Iterator;
+use std::thread;
+
+lazy_static::lazy_static! {
+static ref UMI_PATTERN: regex::Regex = regex::Regex::new("^(N{2,})([ATCG]*)$").unwrap();
+}
+struct Nucleotide {
+    offset: usize,
+    spacer: String,
+}
+enum ExtractedRecord {
+    Empty,
+    Valid {
+        read: bio::io::fastq::Record,
+        umi: Vec<u8>,
+    },
+}
+fn read_fastq(
+    path: &std::string::String,
+) -> bio::io::fastq::Reader<std::io::BufReader<std::fs::File>> {
+    std::fs::File::open(path)
+        .map(bio::io::fastq::Reader::new)
+        .unwrap()
+}
+fn output_file(name: &str) -> bio::io::fastq::Writer<std::fs::File> {
+    std::fs::File::create(format!("{}.fastq", name))
+        .map(bio::io::fastq::Writer::new)
+        .unwrap()
+}
+
+#[derive(clap::Parser)]
+struct Opts {
+    #[clap(long, default_value = "integrated")]
+    prefix: String,
+    #[clap(long, required = true)]
+    r1_in: Vec<String>,
+    #[clap(long)]
+    r2_in: Vec<String>,
+    #[clap(subcommand)]
+    sub: Commands,
+}
+
+#[derive(clap::Subcommand)]
+enum Commands {
+    #[clap(name = "separate")]
+    Separate {
+        #[clap(long, required = true)]
+        ru_in: Vec<String>,
+    },
+    #[clap(name = "inline")]
+    Inline {
+        #[clap(long, required = true)]
+        pattern1: String,
+        #[clap(long)]
+        pattern2: Option<String>,
+    },
+}
+
+fn write_to_file(
+    input: bio::io::fastq::Record,
+    mut output: bio::io::fastq::Writer<std::fs::File>,
+    umi: &[u8],
+    second: bool,
+) -> bio::io::fastq::Writer<std::fs::File> {
+    let s = input;
+    if second {
+        let header = &[s.id(), ":", std::str::from_utf8(&umi).unwrap()].concat();
+        let mut string = String::from(s.desc().unwrap());
+        string.replace_range(0..1, "2");
+        let desc: Option<&str> = Some(&string);
+        output.write(&header, desc, s.seq(), s.qual()).unwrap();
+    } else {
+        let header = &[s.id(), ":", std::str::from_utf8(&umi).unwrap()].concat();
+        output.write(&header, s.desc(), s.seq(), s.qual()).unwrap();
+    }
+    output
+}
+fn parse(pattern: &str) -> Option<Nucleotide> {
+    if let Some(captures) = UMI_PATTERN.captures(pattern) {
+        Some(Nucleotide {
+            offset: captures.get(1)?.end(),
+            spacer: captures.get(2)?.as_str().into(),
+        })
+    } else {
+        panic!("")
+    }
+}
+fn extract(record: bio::io::fastq::Record, pattern: &str) -> ExtractedRecord {
+    let handler = parse(pattern);
+    match handler {
+        Some(Nucleotide { offset, spacer }) => {
+            let end = offset + spacer.len();
+            if end <= record.seq().len() && record.seq()[offset..end] == *spacer.as_bytes() {
+                let read = bio::io::fastq::Record::with_attrs(
+                    record.id(),
+                    record.desc(),
+                    record.seq()[end..record.seq().len()].into(),
+                    record.qual()[end..record.qual().len()].into(),
+                );
+                ExtractedRecord::Valid {
+                    read: read,
+                    umi: record.seq()[0..offset].into(),
+                }
+            } else {
+                ExtractedRecord::Empty
+            }
+        }
+        None => panic!(""),
+    }
+}
+fn write_inline_to_file(
+    record: ExtractedRecord,
+    write_file: bio::io::fastq::Writer<std::fs::File>,
+    second: bool,
+) -> bio::io::fastq::Writer<std::fs::File> {
+    match record {
+        ExtractedRecord::Empty => panic!("Not Valid UMI/ Record"),
+        ExtractedRecord::Valid { read, umi } => write_to_file(read, write_file, &umi, second),
+    }
+}
+fn main() {
+    let args = Opts::parse();
+
+    // Create write files
+    let mut write_file_r1 = output_file(&format!("{}1", &args.prefix));
+
+    // read supplied files
+    let r1 = read_fastq(&args.r1_in[0]).records();
+    match args.sub {
+        Commands::Separate { ru_in } => {
+            let ru1 = ru_in.clone();
+            let handle1 = thread::spawn(move || {
+                let ru = read_fastq(&ru_in[0]).records();
+                for (r1_rec, ru_rec) in r1.zip(ru) {
+                    write_file_r1 =
+                        write_to_file(r1_rec.unwrap(), write_file_r1, ru_rec.unwrap().seq(), false);
+                }
+            });
+            let mut l = Vec::new();
+            l.push(handle1);
+            if !&args.r2_in.is_empty() {
+                let r2 = read_fastq(&args.r2_in[0]).records();
+                let mut write_file_r2 = output_file(&format!("{}2", &args.prefix));
+                let handle2 = thread::spawn(move || {
+                    let ru = read_fastq(&ru1[0]).records();
+                    for (r2_rec, ru_rec) in r2.zip(ru) {
+                        write_file_r2 = write_to_file(
+                            r2_rec.unwrap(),
+                            write_file_r2,
+                            ru_rec.unwrap().seq(),
+                            true,
+                        );
+                    }
+                });
+                l.push(handle2);
+            }
+            for i in l {
+                if !i.is_finished() {
+                    i.join().unwrap();
+                }
+            }
+        }
+        Commands::Inline { pattern1, pattern2 } => {
+            let handle1 = thread::spawn(move || {
+                for r1_rec in r1 {
+                    let record1 = extract(r1_rec.unwrap(), &pattern1);
+                    write_file_r1 = write_inline_to_file(record1, write_file_r1, false);
+                }
+            });
+            let mut l = Vec::new();
+            l.push(handle1);
+
+            if !&args.r2_in.is_empty() {
+                let mut write_file_r2 = output_file(&format!("{}2", &args.prefix));
+                let r2 = read_fastq(&args.r2_in[0]).records();
+                let handle2 = thread::spawn(move || {
+                    for r2_rec in r2 {
+                        let record2 = extract(r2_rec.unwrap(), &(pattern2.as_ref().unwrap()));
+                        write_file_r2 = write_inline_to_file(record2, write_file_r2, true);
+                    }
+                });
+                l.push(handle2);
+            }
+            for i in l {
+                if !i.is_finished() {
+                    i.join().unwrap();
+                }
+            }
+        }
+    }
+}