fastquality

Inspiration

We were inspired to address the an aspect of the difficulty surrounding assembling DNA sequences. More accurate and efficient programs can help with DNA analysis which is used in a variety of real-world contexts.

What it does

Our program aims to clean up fastq files so that these DNA reads can be ready to assemble into a single sequence.

How we built it

This program was written fully in Java.

Challenges we ran into

We ran into challenges with time and gaps in our scientific knowledge. We spent a lot of time doing research as a result.

Accomplishments that we're proud of

We are proud of being able to analyze large fastq files (~600 MB) in less than five minutes!

What we learned

We learned a lot about the process of DNA sequence alignment. We also learned about the fastq file format and how to parse it in a program.

What's next for fastquality

We would love to continue to make further optimizations that will make the fastq file more accurate. This could involve removing redundant reads and checking for uniform GC content to ensure the data is good quality. We also envision incorporating this program with an aligner.

Built With

• java