ArticleBMC research notes2017
fastQ_brew: module for analysis, preprocessing, and reformatting of FASTQ sequence data.
Article in BMC research notes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed.
- A chromosome-level genome assembly of the South African indigenous, Kolbroek pig, Sus scrofa domesticus.Scientific data · 2026Article
- Whole-genome sequencing ofMicrobiology resource announcements · 2025Article
- Phylogenetic Reassessment of Murinae Inferred from the Mitogenome of the Monotypic GenusBiology · 2025Article
- Characteristics of the Dynamic Evolutionary Pathway of ADSCs Induced Differentiation into Astrocytes Based on scRNA-Seq Analysis.Molecular neurobiology · 2025Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Article
- Read trimming has minimal effect on bacterial SNP-calling accuracy.Microbial genomics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing datasets are stored as FASTQ formatted files. In order to avoid downstream artefacts, it is critical to implement a robust preprocessing protocol of the FASTQ sequence in order to determine the integrity and quality of the data.
resultsHere I describe fastQ_brew which is a package that provides a suite of methods to evaluate sequence data in FASTQ format and efficiently implements a variety of manipulations to filter sequence data by size, quality and/or sequence. fastQ_brew allows for mismatch searches to adapter sequences, left and right end trimming, removal of duplicate reads, as well as reads containing non-designated bases. fastQ_brew also returns summary statistics on the unfiltered and filtered FASTQ data, and offers FASTQ to FASTA conversion as well as FASTQ reverse complement and DNA to RNA manipulations.
conclusionsfastQ_brew is open source and freely available to all users at the following webpage: https://github.com/dohalloran/fastQ_brew .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.