Tutorials

These vignettes demonstrate how some of the compgen.io tools can be used for data analysis in practice. Often these tools are used in conjunction with other software to produce an analysis workflow/pipeline.

If you have questions or ideas for other tutorials, please let me know.

• File formats – Description of common file formats used in NGS analysis

• FASTQ pre-processing – Trimming bad sequence before alignment (DNA & RNA)

  ngsutilsj

  bwa

• Docker with cgpipe – Integrating Docker containers with CGPipe jobs

  cgpipe

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Table of contents

• Tutorial: File formats
• Tutorial: FASTQ Pre-processing
• Tutorial: Docker with cgpipe