Sequence Data QC Pipeline
A sequencing run just landed and nobody trusts the data yet. Build the parse, clean, filter, trim and quality-check steps that turn raw files into data you can use.
The brief
Sequencing machines do not hand you tidy answers. They produce large files of reads with typos, leftover adapters, low-quality stretches and the occasional broken record. Before any real analysis, every bioinformatician runs the data through quality control (QC).
You have just received a batch of files from a sequencing run. Over five stages you build the QC pipeline in the order the data really flows: read the file, clean and check each record, filter out short ones, trim adapters off reads and finally judge read quality from a FASTQ file.
WHAT YOU WILL BUILD
A small QC pipeline: a FASTA reader, a record cleaner and validator, a length filter, an adapter trimmer and a FASTQ quality checker.
How a lab works
- Read the stage brief and look at the given input.
- Write code in a notebook that runs on your own computer, using skills from the problem bank.
- Submit your code and explanation. We re-run the code on our server against hidden tests, so the result can be trusted.
- Check your understanding with a few questions (a self-check in your browser) and explain your approach in your own words.
- Finish every stage and the lab is marked completed.
What you'll learn
- Parse the FASTA and FASTQ formats, the standard ways sequences are stored
- Clean and validate records so bad input never reaches later steps
- Filter and trim reads the way real sequencing pipelines do
- Use Phred quality scores to decide how far to trust a read
Skills from the problem bank
This project builds on techniques practised in these problems. Solving them first is recommended, not required.
- Multi-FASTA Parser Foundational
- Validating Sequence Records Intermediate
- Sequence Sanitiser Foundational
- Filter Sequences by Length Foundational
- Trim Adapter Sequences Foundational
- Sequence Report Card Foundational
- FASTQ Quality Control Intermediate