An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology

By R. Henrik Nilsson, Vilmar Veldre, Martin Hartmann, M. Unterseher, A. Amend, J. Bergsten, Erik Kristiansson, Martin Ryberg, A. Jumpponen, Kessy Abarenkov. 2010

224 citations recorded by the source corpus.

Subfields: Cell Biology, Molecular Biology, Plant Science

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

In Molecular Biology

In Plant Science

Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “Each sequence has either ITS1 or ITS2 region only, extracted from 454 pyrosequencing data using FungalITSextractor (Nilsson et al. 2010).”
Long-term changes in soil microbial communities during primary succession (2014, methodology): “Following this initial clean-up, the ITS1 region was extracted using the ITS 225 Extractor tool on the PlutoF Workbench (Abarenkov et al., 2010b; Nilsson et al., 2010) and 226 sequences shorter than 100 bp following this step were discarded.”
Scraping the bottom of the barrel: are rare high throughput sequences artifacts? (2015, methodology): “…sequences for each ITS OTU (including singletons) using the online UNITE Phylogenetic Module ITSx using default online options with the exception that we set the minimal number of domains required to match for extraction to one (unite.ut.ee; Nilsson et al., 2010; Bengtsson-Palme et al., 2013).”
Distinct soil microbial diversity under long-term organic and conventional farming (2014, methodology): “…al. (2014), including elimination of sequencing errors (Quince et al., 2009), PCR substitution errors (Quince et al., 2011) and chimeras (Edgar et al., 2011) as implemented in MOTHUR (Schloss et al., 2009), as well as target verification and extraction (Hartmann et al., 2010; Nilsson et al., 2010).”
Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances (2013, methodology): “Sequences were denoised in one batch using the flowgram clustering algorithm (Reeder and Knight, 2010), and the ITS1 spacer was extracted from the sequence (Nilsson et al., 2010) and used as the basis for comparison.”
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015, unknown): “Cloning of ribosomal ITS PCR products creates frequent... 47 emerencia.org/chimerachecker.html (Nilsson et al. 2010).”
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data (2013, methodology): “Nilsson et al. (2010a) released a UNIX software package – Fungal ITS Extractor – to automatically identify, annotate and extract ITS1 and ITS2 from fungal ITS sequences.”