2FAST2Q: a general-purpose sequence search and counting program for FASTQ files.
Details
State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_A58E06840055
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
2FAST2Q: a general-purpose sequence search and counting program for FASTQ files.
Journal
PeerJ
ISSN
2167-8359 (Print)
ISSN-L
2167-8359
Publication state
Published
Issued date
2022
Peer-reviewed
Oui
Volume
10
Pages
e14041
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Publication Status: epublish
Abstract
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.
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.
Using published CRISPRi datasets in which Escherichia coli and Mycobacterium tuberculosis gene essentiality, as well as host-cell sensitivity towards SARS-CoV2 infectivity were tested, we demonstrate that 2FAST2Q efficiently recapitulates published output in read counts per provided feature. We further show that 2FAST2Q can be used in any experimental setup that requires feature extraction from raw reads, being able to quickly handle Hamming distance based mismatch alignments, nucleotide wise Phred score filtering, custom read trimming, and sequence searching within a single program. Moreover, we exemplify how different FASTQ read filtering parameters impact downstream analysis, and suggest a default usage protocol. 2FAST2Q is easier to use and faster than currently available tools, efficiently processing not only CRISPRi-seq / random-barcode sequencing datasets on any up-to-date laptop, but also handling the advanced extraction of de novo features from FASTQ files. We expect that 2FAST2Q will not only be useful for people working in microbiology but also for other fields in which amplicon sequencing data is generated. 2FAST2Q is available as an executable file for all current operating systems without installation and as a Python3 module on the PyPI repository (available at https://veeninglab.com/2fast2q).
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.
Using published CRISPRi datasets in which Escherichia coli and Mycobacterium tuberculosis gene essentiality, as well as host-cell sensitivity towards SARS-CoV2 infectivity were tested, we demonstrate that 2FAST2Q efficiently recapitulates published output in read counts per provided feature. We further show that 2FAST2Q can be used in any experimental setup that requires feature extraction from raw reads, being able to quickly handle Hamming distance based mismatch alignments, nucleotide wise Phred score filtering, custom read trimming, and sequence searching within a single program. Moreover, we exemplify how different FASTQ read filtering parameters impact downstream analysis, and suggest a default usage protocol. 2FAST2Q is easier to use and faster than currently available tools, efficiently processing not only CRISPRi-seq / random-barcode sequencing datasets on any up-to-date laptop, but also handling the advanced extraction of de novo features from FASTQ files. We expect that 2FAST2Q will not only be useful for people working in microbiology but also for other fields in which amplicon sequencing data is generated. 2FAST2Q is available as an executable file for all current operating systems without installation and as a Python3 module on the PyPI repository (available at https://veeninglab.com/2fast2q).
Keywords
2FAST2Q, Barcode-seq, Bioinformatics, CRISPRi, CRISPRi-seq, FASTQ, Python, Sequencing analysis, Tn-seq
Pubmed
Open Access
Yes
Create date
08/11/2022 10:16
Last modification date
23/10/2023 11:29