aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.

"both databases are publicly available to the wider scientific community through the scilifelab figshare at https://doi org/10 17044/scilifelab 20205504 and https://doi org/10 17044/scilifelab 20518251 .; the workflow together with installation instructions examples of command lines documentation vignettes and test dataset can be accessed from github https://github com/nbisweden/ameta [ ] and zenodo https://zenodo org/record/8354933 [ ] ameta was developed as a collection of snakemake rules listed in a snakefile according to the snakemake best practices ( https://snakemake readthedocs io/en/stable/snakefiles/best_practices html#snakefiles-best-practices ) and workflow template ( https://github com/snakemake-workflows/snakemake-workflow-template ).; the codes used for generating ground truth microbial abundances as well as simulating ancient metagenomic reads are available on github: https://github com/nikolayoskolkov/ameta via zenodo https://doi org/10 5281/zenodo 8130819 .; availability of data and materials the workflow is publicly available at https://github com/nbisweden/ameta [ 50 ] and also deposited in a zenodo repository https://zenodo org/record/8354933 [ 51 ].; the non-redundant ncbi nt krakenuniq database can be accessed at the scilifelab figshare following the address: https://doi org/10 17044/scilifelab 20205504 and the microbial version of ncbi nt combined with human and complete eukaryotic reference genomes can be accessed via scilifelab figshare at https://doi org/10 17044/scilifelab 20518251 .; further the bowtie2 index of ncbi nt is publicly available through scilifelab figshare at https://doi org/10 17044/scilifelab 21070063 and the pathogenic microbial subset of this index can be accessed via the scilifelab figshare at https://doi org/10 17044/scilifelab 21185887 .; codes for computer simulations and other scripts used for this article can be accessed at https://github com/nikolayoskolkov/ameta and via zenodo https://doi org/10 5281/zenodo 8130819 .; finally the simulated metagenomic dataset with known ground truth used for benchmarking ameta against hops is accessible via scilifelab figshare link https://doi org/10 17044/scilifelab 21261405 and the simulated dataset enriched for microbial pathogenic species is available at https://doi org/10 17044/scilifelab 24211584 . the workflow together with installation instructions examples of command lines documentation vignettes and test dataset can be accessed from github https://github com/nbisweden/ameta [ ] and zenodo https://zenodo org/record/8354933 [ ] ameta was developed as a collection of snakemake rules listed in a snakefile according to the snakemake best practices ( https://snakemake readthedocs io/en/stable/snakefiles/best_practices html#snakefiles-best-practices ) and workflow template ( https://github com/snakemake-workflows/snakemake-workflow-template ).; availability of data and materials the workflow is publicly available at https://github com/nbisweden/ameta [ 50 ] and also deposited in a zenodo repository https://zenodo org/record/8354933 [ 51 ]. availability of data and materials the workflow is publicly available at https://github com/nbisweden/ameta [ 50 ] and also deposited in a zenodo"

"the workflow together with installation instructions examples of command lines documentation vignettes and test dataset can be accessed from github https://github com/nbisweden/ameta [ ] and zenodo https://zenodo org/record/8354933 [ ] ameta was developed as a collection of snakemake rules listed in a snakefile according to the snakemake best practices ( https://snakemake readthedocs io/en/stable/snakefiles/best_practices html#snakefiles-best-practices ) and workflow template ( https://github com/snakemake-workflows/snakemake-workflow-template ).; the codes used for generating ground truth microbial abundances as well as simulating ancient metagenomic reads are available on github: https://github com/nikolayoskolkov/ameta via zenodo https://doi org/10 5281/zenodo 8130819 .; availability of data and materials the workflow is publicly available at https://github com/nbisweden/ameta [ 50 ] and also deposited in a zenodo repository https://zenodo org/record/8354933 [ 51 ].; codes for computer simulations and other scripts used for this article can be accessed at https://github com/nikolayoskolkov/ameta and via zenodo https://doi org/10 5281/zenodo 8130819 ."

"Declarations Ethics approval and consent to participateNot applicable. Consent for publicationNot applicable. Competing interestsThe authors declare that they have no competing interests. Competing interests The authors declare that they have no competing interests."

"Funding Open access funding provided by Lund University. NO, PU, and CM are financially supported by Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC), partially funded by the Swedish Research Council through grant agreement no. 2018–05973, in particular projects: SNIC 2021/5–335, SNIC 2021/6–260, SNIC 2022/5–100, SNIC 2022/6–46, SNIC 2022/22–507, SNIC 2022/23–275, and Mersin University BAP project 2019–3-AP3-3729. AG is financially supported by the Swedish Research Council (VR; 2019–00849)."