This repository is dedicated to the development of CRISPRi systems for enteric gram-negative bacteria. It aims to streamline the integration of CRISPRi into the genetic makeup of these organisms, facilitating advanced research and applications.
For project documentation and more detailed information, please visit our wiki page.
The tools developed for this project, including sequence processing and analysis utilities, are hosted at barcoder. Among these tools is heuristicount, a component of barcoder designed for accurate read counting. It analyzes the orientation, size, position, and valid context of reads, efficiently processing both .fastq and .reads.zst files.
Sequences within this repository are compressed using a custom format, *.reads.zst. This method, implemented via barcoder.distillreads, not only significantly reduces file sizes to 5-10% of their original volume but also applies pairwise sorting of reads to further reduce their size. This format encapsulates a streamlined list of reads in .zst compression, omitting the additional metadata typically found in .fastq files.
For further inquiries or contributions, please refer to the wiki or raise an issue in the repository.