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SH information from UNITE databases

dataset
posted on 13.05.2022, 08:27 authored by Jeanette TångrotJeanette Tångrot

The data is the result of querying the PlutoF API (https://plutof.docs.apiary.io, Abarenkov et al 2010) with all sequence names in the UNITE general FASTA release (https://doi.org/10.15156/BIO/786368; Abarenkov et al. 2020, https://doi.org/10.15156/BIO/1280049; Abarenkov et al. 2021), in order to find the sequence hypothesis (SH) at level 1.5, version 8, for each sequence, resulting in a sequence-to-SH matching file (*.seq2SH.tsv). For each SH, the complete taxonomy is extracted from PlutoF by querying the PlutoF API, and stored in the *.SH.tax files.

Files are available for UNITE version 8.2; sh_general_release_dynamic_04.02.2020.seq2sh.tsv.bz2 containing sequence to SH matchings, and sh_general_release_dynamic_04.02.2020.SHs.tax.bz2 containing SH taxonomies, and for UNITE version 8.3; sh_general_release_dynamic_10.05.2021.seq2sh.tsv.bz2 and sh_general_release_dynamic_10.05.2021.SHs.tax.bz2. All files are tab separated text files compressed with bzip2.

Corresponding files are also available for the all eukaryotes version if the UNITE database (https://doi.org/10.15156/BIO/786370; Abarenkov et al 2020b, https://doi.org/10.15156/BIO/1280127; Abarenkov et al 2021b)

Assignment of species hypothesis to ITS amplicons using this data and the UNITE general FASTA release is available as an optional argument to the nf-core/ampliseq Nextflow workflow from version 2.3.2: `--addsh` together with `--dada_ref_taxonomy unite-fungi` (https://nf-co.re/ampliseq; Straub et al. 2020).


Generation of files
After download and file extraction of the UNITE general FASTA release, each sequence name in the fasta file was used as query to PlutoF to find which SH at level 1.5 in release 8 the sequence belongs to, in order to generate the *.seq2sh.tsv files with sequence to SH matchings. Each SH was subsequently used as query to PlutoF to extract the complete taxonomy for the SH, stored in the *.SHs.tax files.
Two python scripts for automatic querying and generation of the files can be found in the `scripts` folder in the GitHub repo: https://github.com/biodiversitydata-se/unite-shinfo. See the accompanying README file for usage information.

Funding

Swedish Biodiversity Data Infrastructure

Swedish Research Council

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History

Publisher

Swedish Biodiversity Data Infrastructure (SBDI)