11.15. De Novo Sequence Assembly - Clara Genomics Analysis

This is a reference pipeline using Clara Genomic Analysis tools to assemble genome with Clara Deploy SDK.

These tools exploit the abilities of GPU to accelerate gene sequencing.


api-version: 0.3.0 name: denovo-gpu parameters: DOCKER_IMAGE: claraomics/cga_cuda10 DOCKER_TAG: 0.4.3 MAPPER_THREADS: 15 MAPPER_KMER_SIZE: 15 MAPPER_WINDOW_SIZE: 5 MAPPER_INDEX_SIZE: 8000 MAPPER_ADDITIONAL_PARAMS: '' RACON_LOOPS: 5 RACON_THREADS: 5 RACON_POLISH_BATCH_SIZE: 4 RACON_ADDITIONAL_PARAMS: '' JOB_ID: '.' operators: - name: mapper description: CUDA mapper container: image: ${{DOCKER_IMAGE}} tag: ${{DOCKER_TAG}} command: ["/bin/sh", "-c", "mapperWrapper.sh${{MAPPER_ADDITIONAL_PARAMS}}-i/input-d/mapperOutput/${{JOB_ID}}-o/mapperOutput/${{JOB_ID}}/overlaps.paf-t${{MAPPER_THREADS}}-k${{MAPPER_KMER_SIZE}}-w${{MAPPER_WINDOW_SIZE}}-s${{MAPPER_INDEX_SIZE}}"] requests: gpu: 1 input: - path: /input/ output: - path: /mapperOutput - name: miniasm description: Miniasm container: image: ${{DOCKER_IMAGE}} tag: ${{DOCKER_TAG}} command: ["/bin/sh", "-c", "miniasmWrapper.sh-f/mapperOutput/${{JOB_ID}}/sample.fasta-l/mapperOutput/${{JOB_ID}}/overlaps.paf-o/asmOutput/${{JOB_ID}}/reads.gfa"] input: - path: /input/ - from: mapper path: /mapperOutput output: - path: /asmOutput - name: racon description: Polish Assembly using racon container: image: ${{DOCKER_IMAGE}} tag: ${{DOCKER_TAG}} command: ["/bin/sh", "-c", "raconWrapper.sh${{RACON_ADDITIONAL_PARAMS}}-r/mapperOutput/${{JOB_ID}}/sample.fasta-t${{RACON_THREADS}}-l${{RACON_LOOPS}}-p${{RACON_POLISH_BATCH_SIZE}}-f/asmOutput/${{JOB_ID}}/reads.gfa-o/raconOutput/${{JOB_ID}}-a/raconOutput/${{JOB_ID}}/polished_assembly.fa"] requests: gpu: 1 input: - path: /input/ - from: miniasm path: /asmOutput - from: mapper path: /mapperOutput output: - path: /raconOutput/

Please refer to the Run Reference Pipelines using Local Input Files in the How to run a Reference Pipeline section to learn how to register a pipeline and execute the pipeline using local input files.

Input requires a folder containing the following files:

  • sample.fasta - Input fasta sample file for all-to-all mapping

  • jobConfig(optional) - A file containing param and value in shell script style. A sample (sample_job_config.sh) is provided. Following is content of a jobConfig file with default values.


    KMER_SIZE=15 # length of kmer to use for minimizers WINDOW_SIZE=5 # length of window to use for minimizers INDEX_SIZE=10000 # length of batch size used for query RACON_LOOPS=5 # Number of polishing loops RACON_THREADS=15 # number of threads POLISH_BATCH_SIZE=6 # number of batches for CUDA accelerated polishing

Assembled and polished sequence

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