obitools: a unix‐inspired software package for DNA metabarcoding

By Frédéric Boyer, C. Mercier, Aurélie Bonin, Yvan Le Bras, P. Taberlet, É. Coissac. Molecular Ecology Resources, 2016

1,025 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/1d2e51d1fc17c80f694ad0d1a95cd0f2bfe2470b

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Citations in the corpus

From environmental DNA sequences to ecological conclusions: How strong is the influence of methodological choices? (2019, methodology): “We finally assigned each remaining sequence to a taxonomic clade with the ecotag command from the OBITools software package (Boyer et al., 2016) that uses a lowest common ancestor algorithm for the assignment, and the EMBL database version 133 as a reference.”
Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, methodology): “The analysis of the DNA data relies on a variety of bioinformatics tools, of which QIIME, MOTHUR, and OBITOOLS are among the most commonly used (Boyer et al., 2016; Caporaso et al., 2010; Schloss et al., 2009).”
Bats as potential suppressors of multiple agricultural pests: A case study from Madagascar (2019, methodology): “Bioinformatic analyses were performed using the OBITools metabarcoding software suite (Boyer et al., 2016).”
Species-specific detection and quantification of environmental DNA from marine fishes in the Baltic Sea (2019, methodology): “The specificity of the primers was also tested using OBITools (Boyer et al., 2016) and ecoPCR (Bellemain et al.”
Large‐scale DNA‐based survey of frogs in Amazonia suggests a vast underestimation of species richness and endemism (2020, methodology): “The resulting outputs were analysed with the OBITOOLS software suite (Boyer et al., 2016).”
GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding (2021, methodology): “This database was formatted using obiconvert from the OBITOOLs toolkit (Boyer et al., 2016) to run in silico PCRs (i.e. virtual PCR based on primer affinity to sequences).”
Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding (2016, methodology): “Finally, the length distribution of the amplified sequences (excluding primers) was analysed using the OBITOOLS package (http://metabarcoding.org/obitools; Boyer et al. 2015).”
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities (2017, methodology): “…that of microbial data sets and can be acquired using packages developed either for microbial (Caporaso et al., 2010) or for macro-organism data (Boyer et al., 2016), but taxonomic assignment will require a robust data set of locus-specific reference sequences and the associated taxonomic data…”