> For the complete documentation index, see [llms.txt](https://docs.abi.am/abi-omicss-guide-2021/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/fastqc.md). # FastQC Modern high throughput sequencers can generate tens of millions of sequences in a single run. Before analyzing this sequence to draw biological conclusions you should always perform some simple quality control checks to ensure that the raw data looks good and there are no problems or biases in your data that may affect how you can usefully use it. Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems that were generated by the sequencer itself. FastQC aims to provide a QC report which can spot problems that originate either in the sequencer or in the starting library material. We are going to use FastQC in the scope of this guide, so make sure to thoroughly review the following content. ### [The FastQC Manual](https://dnacore.missouri.edu/PDF/FastQC_Manual.pdf) ### [FastQC Installation Instructions (txt)](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt) ### FastQC Documentation (.pptx below) {% embed url="" %} ### Using FastQC to Check the Quality of Throughput Sequence {% embed url="" %} ## Congratulations! If you made it here, then congratulations! You have successfully completed this section. Move to the next portion of the guide with the arrow buttons below. --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter: ``` GET https://docs.abi.am/abi-omicss-guide-2021/week-6/ngs/fastqc.md?ask=&goal= ``` `ask` is the immediate question: it should be specific, self-contained, and written in natural language. `goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.