Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes

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Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is process your data with a broad set of tools, so that you can get to the fun part of analyses quicker!

https://bactopia.github.io/v2.2.0/ https://journals.asm.org/doi/10.1128/mSystems.00190-20 https://bactopia.github.io/acknowledgements/

  1. Tools and databases for running bactopia #7.2 G data are under (bincs) xxxx@hamburg:~/.bactopia/singularity$ #which are tools and databases for running bactopia bactopia-annotate_genome-1.6.1.img bactopia-antimicrobial_resistance-1.6.1.img bactopia-ariba_analysis-1.6.1.img bactopia-assemble_genome-1.6.1.img bactopia-assembly_qc-1.6.1.img bactopia-call_variants-1.6.1.img bactopia-count_31mers-1.6.1.img bactopia-download_references-1.6.1.img bactopia-gather_fastqs-1.6.1.img bactopia-minmers-1.6.1.img bactopia-qc_reads-1.6.1.img bactopia-sequence_type-1.6.1.img dockerhub-images-built-1.6.1.txt * /home/xxx/anaconda3/envs/bactopia /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/annotate_genome-2.2.x /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/assemble_genome-2.2.x /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/assembly_qc-2.2.x /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/bioconda--csvtk-0.25.0 /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/bioconda--multiqc-1.11 /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/call_variants-2.2.x /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/gather_samples-2.2.x /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs/minmers-2.2.x

  2. Software dependencies of Bactopia (SUCCESSFUL) bactopia datasets --species "Enterococcus faecium" --include_genus --skip_amr (bactopia) xxx@hamm:~/DATA/Data_Holger_VRE$ bactopia --list_wfs (bactopia) xxx@hamm:~/DATA/Data_Holger_VRE$ bactopia download --use_defaults --force_rebuild (bactopia) xxx@hamm:~/DATA/Data_Holger_VRE$ bactopia --samples samples.txt --datasets datasets --outdir "/home/xxx/DATA/Data_Holger_VRE/results_bactopia" --species 'Enterococcus faecium' -resume 2022-12-20 16:03:59:root:INFO - Checking if environment pre-builds are needed, use --verbose to see full details. 2022-12-20 16:03:59:root:INFO - Found Conda environments in /home/jhuang/anaconda3/envs/bactopia/share/bactopia-2.2.x/conda/envs, if a complete rebuild is needed please use --force_rebuild N E X T F L O W ~ version 22.10.1 Launching /home/xxx/anaconda3/envs/bactopia/share/bactopia-2.2.x/main.nf [amazing_keller] DSL2 - revision: 145bb11899

Bactopia is truly a case of "standing upon the shoulders of giants". Bactopia currently includes more than 140 datasets and software packages. Nearly every component uses, from the workflow, datasets, software packages, even the framework for this site, was created by others and made freely available to the public.

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