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Citations

NextITS

Mikryukov V., Anslan S., Tedersoo L. NextITS: a pipeline for metabarcoding fungi and other eukaryotes with full-length ITS sequenced with PacBio. https://github.com/vmikk/NextITS, doi: 10.5281/zenodo.15074881

Nextflow

Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.

Pipeline tools

Core tools

  • ITSx

    Bengtsson-Palme, J., Ryberg, M., Hartmann, M., Branco, S., Wang, Z., Godhe, A., De Wit, P., Sánchez-García, M., Ebersberger, I., de Sousa, F., Amend, A., Jumpponen, A., Unterseher, M., Kristiansson, E., Abarenkov, K., Bertrand, Y.J.K., Sanli, K., Eriksson, K.M., Vik, U., Veldre, V. and Nilsson, R.H.. Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data. Methods Ecol Evol 2013, 4: 914-919. doi: 10.1111/2041-210X.12073.

  • VSEARCH

    Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016 4:e2584. doi: 10.7717/peerj.2584

  • VSEARCH option usearch_global implements the USEARCH algorithm

    Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010 26(19) 2460-2461

  • Cutadapt

    Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal 17.1 (2011): pp-10. doi: 10.14806/ej.17.1.200.

Database for reference-based chimera removal

  • EUKARYOME database

    Tedersoo L, Hosseyni Moghaddam MS, Mikryukov V, Hakimzadeh A, Bahram M, Nilsson RH, Yatsiuk I, Geisen S, Schwelm A, Piwosz K, Prous M, Sildever S, Chmolowska D, Rueckert S, Skaloud P, Laas P, Tines M, Jung J-H, Choi JH, Alkahtani S, Anslan S (2024). EUKARYOME: The rRNA gene reference database for identification of all eukaryotes. Database, 2024, baae043. doi: 10.1093/database/baae043

Taxonomic classification and databases

Abarenkov K, Nilsson RH, Larsson K-H, Taylor AFS, May TW, Frøslev TG, Pawlowska J, Lindahl B, Põldmaa K, Truong C, Vu D, Hosoya T, Niskanen T, Piirmann T, Ivanov F, Zirk A, Peterson M, Cheeke TE, Ishigami Y, Jansson AT, Stjernegaard Jeppesen T, Kristiansson E, Mikryukov V, Miller JT, Oono R, Ossandon FJ, Paupério J, Saar I, Schigel D, Suija A, Tedersoo L, Kõljalg U (2023). The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: Sequences, taxa and classifications reconsidered. Nucleic Acids Research, gkad1039. doi: 10.1093/nar/gkad1039

Software packaging/containerisation tools

  • Docker

  • Singularity

    Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.