denniswiersma/SGBS

Issues

• Implement multithreading

  #28 opened a year ago by denniswiersma
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• Implement rule for variant calling with `platypus`

  #27 opened a year ago by denniswiersma
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• Implement rule for sorting BAM files using `samtools sort`

  #23 opened a year ago by denniswiersma
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• Implement rule for converting SAM files to BAM files with `samtools view`

  #24 opened a year ago by denniswiersma
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• Implement rule for indexing BAM files with `samtools index`

  #25 opened a year ago by denniswiersma
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• Implement rule for aligning reads with `bwa mem`

  #21 opened a year ago by denniswiersma
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• implement rule for trimming adapter sequences with `flexbar`

  #20 opened a year ago by denniswiersma
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• Implement rule for demultiplexing using barcodes fasta file with `flexbar`

  #19 opened a year ago by denniswiersma
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• Write rule for indexing the reference genome

  #17 opened a year ago by denniswiersma
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• Create layout for config.yaml

  #15 opened a year ago by denniswiersma
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• Setup snakemake repository structure

  #8 opened a year ago by denniswiersma
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• Write project proposal

  #1 opened a year ago by denniswiersma
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• Describe how to visualise the result.

  #4 opened a year ago by denniswiersma
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• Describe how to test the pipeline.

  #5 opened a year ago by denniswiersma
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• Describe input and output.

  #6 opened a year ago by denniswiersma
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• List a research question

  #7 opened a year ago by denniswiersma
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• Add Fast-GBS research paper to docs

  #9 opened a year ago by denniswiersma
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• Describe every step of the pipeline.

  #3 opened a year ago by denniswiersma
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• Describe source material.

  #2 opened a year ago by denniswiersma
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• Add Conda requirements.yml

  #11 opened a year ago by denniswiersma
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• Allow user to query NCBI for FASTQ file and/or reference genome

  #10 opened a year ago by denniswiersma
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