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The development of this workflow was supported by NFDI4Microbiota 
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The GUNC workflow is a nextflow workflow for the detection of chimerism & contamination in prokaryotic genomes resulting from mis-binning of contigs from unrelated lineages. The workflow is based on the CheckM and GUNC (Genome UNClutterer) tools. GUNC applies an entropy based score on taxonomic assignment and the contig location of all genes in a genome.
This workflow:
Also cite:
Orakov A, Fullam A, Coelho LP, et al. GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biol. 2021;22(1):178. Published 2021 Jun 13. doi:10.1186/s13059-021-02393-0
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043-1055. doi:10.1101/gr.186072.114
Ewels PA, Peltzer A, Fillinger S, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276-278. doi:10.1038/s41587-020-0439-x
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This workflow will be available on the CloWM platform (coming soon).
You can run the pipeline using:
nextflow run gunc \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>The input is a csv samplesheet with your input data that looks as follows:
samplesheet.csv:
id,group,assembler,fasta
test_minigut,0,MEGAHIT,https://github.com/nf-core/test-datasets/raw/mag/assemblies/MEGAHIT-test_minigut.contigs.fa.gz
Each row represents a metagenomic bin.