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Merge pull request #1115 from fraser-combe/racon-minimap2
Update Racon 1.5.0 to include minimap2
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| Original file line number | Diff line number | Diff line change |
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| ARG RACON_VER="1.5.0" | ||
| ARG MINIMAP2_VER="2.28" | ||
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| # Use ubuntu as base image | ||
| FROM ubuntu:jammy AS builder | ||
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| ARG RACON_VER | ||
| ARG MINIMAP2_VER | ||
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| # Install dependencies | ||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| perl \ | ||
| default-jre \ | ||
| gnuplot \ | ||
| libgomp1 \ | ||
| maven \ | ||
| git \ | ||
| wget \ | ||
| python3 \ | ||
| build-essential \ | ||
| cmake \ | ||
| zlib1g-dev \ | ||
| curl \ | ||
| bzip2 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Install Racon | ||
| RUN wget https://github.com/lbcb-sci/racon/archive/refs/tags/${RACON_VER}.tar.gz && \ | ||
| tar -xvf ${RACON_VER}.tar.gz && \ | ||
| cd racon-${RACON_VER} && \ | ||
| mkdir build && \ | ||
| cd build && \ | ||
| cmake -DCMAKE_BUILD_TYPE=Release .. && \ | ||
| make | ||
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| # Add Racon to PATH | ||
| ENV PATH="/racon-${RACON_VER}/build/bin:${PATH}" | ||
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| # Test Racon | ||
| RUN racon_test | ||
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| # Install Minimap2 | ||
| RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \ | ||
| mv minimap2-${MINIMAP2_VER}_x64-linux /usr/local/minimap2 | ||
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| # Add Minimap2 to PATH | ||
| ENV PATH="/usr/local/minimap2:${PATH}" | ||
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| # Test Minimap2 | ||
| RUN minimap2 --version | ||
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| FROM ubuntu:jammy AS app | ||
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| ARG RACON_VER | ||
| ARG MINIMAP2_VER | ||
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| # Metadata | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Racon + Minimap2" | ||
| LABEL racon.version="${RACON_VER}" | ||
| LABEL software.version="Racon-${RACON_VER}, Minimap2-${MINIMAP2_VER}" | ||
| LABEL racon.version="${RACON_VER}" | ||
| LABEL minimap2.version="${MINIMAP2_VER}" | ||
| LABEL description="Racon for assembly polishing and Minimap2 for alignment" | ||
| LABEL website="https://github.com/lbcb-sci/racon, https://github.com/lh3/minimap2" | ||
| LABEL license="https://github.com/lbcb-sci/racon/blob/master/LICENSE, https://github.com/lh3/minimap2/blob/master/LICENSE.txt" | ||
| LABEL maintainer="Fraser Combe" | ||
| LABEL maintainer.email="[email protected]" | ||
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| # Install Python and essential tools | ||
| RUN apt-get update && apt-get install -y \ | ||
| procps \ | ||
| wget \ | ||
| python3 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
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| # Copy Racon and Minimap2 binaries | ||
| COPY --from=builder /racon-${RACON_VER}/build/bin/* /usr/local/bin/ | ||
| COPY --from=builder /usr/local/minimap2/* /usr/local/bin/ | ||
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| RUN mkdir /data | ||
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| WORKDIR /data | ||
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| # Set locale settings | ||
| ENV PATH=${PATH} LC_ALL=C | ||
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| CMD racon --help | ||
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| FROM app AS test | ||
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| # Test Racon and Minimap2 | ||
| RUN racon --help && racon --version && minimap2 --version | ||
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| COPY --from=builder /racon-${RACON_VER}/test/data/* /test/ | ||
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| WORKDIR /test | ||
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| # Minimap2 alignment test | ||
| RUN wget -q https://raw.githubusercontent.com/lh3/minimap2/master/test/MT-human.fa && \ | ||
| wget -q https://raw.githubusercontent.com/lh3/minimap2/master/test/MT-orang.fa && \ | ||
| minimap2 -a MT-human.fa MT-orang.fa > test.sam && \ | ||
| head test.sam | ||
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| # Example polishing workflow | ||
| RUN wget -q https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf && \ | ||
| wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz && \ | ||
| wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz && \ | ||
| minimap2 -x map-ont genome.fna.gz test.fastq.gz > test.paf && \ | ||
| racon -t 2 test.fastq.gz test.paf genome.fna.gz > test_polished.fasta && \ | ||
| head test_polished.fasta |
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| # Racon + Minimap2 Container | ||
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| This container combines [Racon](https://github.com/lbcb-sci/racon) and [Minimap2](https://github.com/lh3/minimap2) for efficient polishing and alignment in long-read assembly workflows. | ||
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| ## Tools Included | ||
| - **Racon**: Polishes long-read assemblies. | ||
| - **Minimap2**: Generates alignments for use with Racon and other polishing tools. | ||
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| ### Code Repositories | ||
| - Racon: [GitHub Repository](https://github.com/lbcb-sci/racon) | ||
| - Minimap2: [GitHub Repository](https://github.com/lh3/minimap2) | ||
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| ## Basic Information | ||
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| ### Racon | ||
| - **Executable**: `racon` | ||
| - **Help**: `racon -h` | ||
| - **Version**: `racon -v` | ||
| - **Description**: | ||
| > Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods that do not include a consensus step. | ||
| ### Minimap2 | ||
| - **Executable**: `minimap2` | ||
| - **Help**: `minimap2 -h` | ||
| - **Version**: `minimap2 --version` | ||
| - **Description**: | ||
| > Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. | ||
| ## Example Usage | ||
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| ```bash | ||
| # Racon general | ||
| racon <sequences> <overlaps> <target sequences> | ||
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| # more specific | ||
| racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly} | ||
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| #Combined Racon and Minimap2 Workflow | ||
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| #Align Reads to Assembly Using Minimap2: | ||
| minimap2 -x map-ont <assembly.fasta> <reads.fastq> > overlaps.paf | ||
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| #polish assembly using Racon | ||
| racon --threads {threads} <reads.fastq> overlaps.paf <assembly.fasta> > polished_assembly.fasta | ||
| ``` | ||
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