data wrangling for
computational genomics


These vignettes demonstrate how some of the 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.

TutorialSoftware used
File formatsDescription of common file formats used in NGS analysis
FASTQ pre-processingTrimming bad sequence before alignment (DNA & RNA)ngsutilsj, bwa
Docker with CGPipeIntegrating Docker containers with CGPipe jobscgpipe