ArticleNucleic acids research2020
FASTQINS and ANUBIS: two bioinformatic tools to explore facts and artifacts in transposon sequencing and essentiality studies.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.Molecular systems biology · 2025Article
- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs.Nature communications · 2024Article
- Development of a Serum-Free Medium To Aid Large-Scale Production ofMicrobiology spectrum · 2023Article
- Enabling low-cost and robust essentiality studies with high-throughput transposon mutagenesis (HTTM).PloS one · 2023Article
- SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome.Nucleic acids research · 2022Article
- Article
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- Identification of putative essential protein domains from high-density transposon insertion sequencing.Scientific reports · 2022Article
- Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification.NAR genomics and bioinformatics · 2021Article
- LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions.Microbial biotechnology · 2021Article
- Is amplification bias consequential in transposon sequencing (TnSeq) assays? A case study with aMicrobial genomics · 2021Article
- Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome.Microbes and infectionArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposon sequencing is commonly applied for identifying the minimal set of genes required for cellular life; a major challenge in fields such as evolutionary or synthetic biology. However, the scientific community has no standards at the level of processing, treatment, curation and analysis of this kind data. In addition, we lack knowledge about artifactual signals and the requirements a dataset has to satisfy to allow accurate prediction. Here, we have developed FASTQINS, a pipeline for the detection of transposon insertions, and ANUBIS, a library of functions to evaluate and correct deviating factors known and uncharacterized until now. ANUBIS implements previously defined essentiality estimate models in addition to new approaches with advantages like not requiring a training set of genes to predict general essentiality. To highlight the applicability of these tools, and provide a set of recommendations on how to analyze transposon sequencing data, we performed a comprehensive study on artifacts corrections and essentiality estimation at a 1.5-bp resolution, in the genome-reduced bacterium Mycoplasma pneumoniae. We envision FASTQINS and ANUBIS to aid in the analysis of Tn-seq procedures and lead to the development of accurate genome essentiality estimates to guide applications such as designing live vaccines or growth optimization.
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