Published September 2, 2024 | Version v1.1.0
Software Open

MAGFlow: A Nextflow pipeline for MAG quality assessment and taxonomical annotation

Creators

  • 1. ROR icon University of Fribourg
  • 2. Swiss Institute of Bioinformatics

Description

MAGFlow is a Nextflow pipeline able to generate the input file for BIgMAG by measuring the quality of metagenomes through multiples tools (BUSCO, CheckM2, GUNC and QUAST) and annotating them taxonomically (GTDB-Tk2).

Files

Files (2.3 MB)

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Additional details

Related works

Compiles
Dataset: 10.5281/zenodo.13628330 (DOI)
Is required by
Software: 10.5281/zenodo.13628741 (DOI)

Dates

Available
2024-05-25
Updated
2024-09-02

Software

Repository URL
https://github.com/jeffe107/MAGFlow
Programming language
Nextflow, Python, Shell
Development Status
Active

References

  • Chklovski, A., Parks, D. H., Woodcroft, B. J., & Tyson, G. W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20(8), 1203–1212.
  • Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2022). GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics, 38(23), 5315–5316.
  • Gurevich, A., Saveliev, V., Vyahhi, N., & Tesler, G. (2013). QUAST: quality assessment tool for genome assemblies. Bioinformatics, 29(8), 1072–1075.
  • Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing Genomic Data Quality and Beyond. Current Protocols, 1(12), e323.
  • Orakov, A., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B., & Bork, P. (2021). GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biology, 22(1), 1–19.
  • DI Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316–319.