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The activity takes FASTQ NGS data files and runs a fun program called FASTQE. This program is very similar to the popular FastQC, however, rather than outputting data plot visualizations of NGS sequence quality, FASTQE outputs emojis signifying the quality of each base call in the file. The activity takes a fundamental yet sort of boring step in NGS analysis and makes it accessible and fun to students without much experience in the field. It is also designed to for students with little to no experience using command line analysis to learn and run a few simple commands. The elated reaction from students when they get a long string of emojis to output after typing a few commands is really cool! The activity also utilizes another command line tool called FASTP for FASTQ file trimming and filtering.

• Spring19 QUBES FASTQE FASTP incubator.docx(DOCX | 1 MB)
• Spring19 QUBES FASTQE & FASTP incubator - Google Docs
• License terms

Researchers should cite this work as follows:

• St. Jacques, R., Maza, M., Enke, R. A. (2019). Intro to Command Line Coding Genomics Analysis. NIBLSE Incubator: Intro to Command Line Coding Genomics Analysis, QUBES Educational Resources. doi:10.25334/Q4P733

  BibTex | EndNote

1. 1 Hour
2. Activity Length
3. Advanced
4. Audience Level
5. bioinformatics
6. C2. Computational concepts
7. C4. Bioinformatics tools
8. C5. Data retrieval
9. C7. Scripting
10. command line
11. data science
12. FASTP
13. FASTQ
14. FASTQE
15. genomics
16. High School
17. Incubated at NIBLSE
18. Instructional Setting
19. introductory
20. Lab
21. Lecture
22. Majors
23. NGS analysis
24. NIBLSE
25. Non-majors
26. programming
27. Teaching material
28. Undergraduate