2FAST2Q: a general-purpose sequence search and counting program for FASTQ files.

ABSTRACT:

Background

The increasingly widespread use of next generation sequencing protocols has brought the need for the development of user-friendly raw data processing tools. Here, we explore 2FAST2Q, a versatile and intuitive standalone program capable of extracting and counting feature occurrences in FASTQ files. Despite 2FAST2Q being previously described as part of a CRISPRi-seq analysis pipeline, in here we further elaborate on the program's functionality, and its broader applicability and functions.

Methods

2FAST2Q is built in Python, with published standalone executables in Windows MS, MacOS, and Linux. It has a familiar user interface, and uses an advanced custom sequence searching algorithm.

Results

Using published CRISPRi datasets in which Escherichia coli an

SUBMITTER: Bravo AM 

PROVIDER: S-EPMC9615965 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature