Hello, I had a question about the

--ancient_dna

parameter and pydamage (I am using mag version 5.5.0) . I was wondering if the pydamage filters our contigs that do not pass ancient DNA authentication before assembling bins? I am looking out the output information of my assembled bins and it looks like some of the bins contain no dna degradation patterns. Here is my code: nf-params.json

{
    "input": "\/projects\/standard\/mnievesc\/zolik006\/01_projects\/01_PIALQ\/02_analysis\/03_Metagenomics\/01_analysi$
    "outdir": "\/projects\/standard\/mnievesc\/zolik006\/01_projects\/01_PIALQ\/02_analysis\/03_Metagenomics\/01_analys$
    "megahit_fix_cpu_1": true,
    "spadeshybrid_fix_cpus": 32,
    "clip_tool": "adapterremoval",
    "save_clipped_reads": true,
    "reads_minlength": 30,
    "host_fasta": "\/projects\/standard\/mnievesc\/shared\/ref_seqs\/human_g1k_v37.fasta",
    "host_fasta_bowtie2index": "\/projects\/standard\/mnievesc\/shared\/ref_seqs",
    "save_hostremoved_reads": true,
    "gtdbtk_single_job": true,
    "gtdb_db": "\/projects\/standard\/mnievesc\/zolik006\/02_refseqs\/10_gtdbtk\/gtdbtk_r232_data.tar.gz",
    "prokka_with_compliance": true,
    "prokka_compliance_centre": "UMN",
    "binning_map_mode": "own",
    "min_contig_size": 500,
    "save_assembly_mapped_reads": true,
    "exclude_unbins_from_postbinning": true,
    "run_checkm": true,
    "checkm_db": "\/projects\/standard\/mnievesc\/zolik006\/02_refseqs\/09_metaWARP\/CheckM_DB",
    "refine_bins_dastool": true,
    "refine_bins_dastool_threshold": 0.299999999999999988897769753748434595763683319091796875,
    "postbinning_input": "refined_bins_only",
    "run_gunc": true,
    "gunc_db": "\/projects\/standard\/mnievesc\/zolik006\/02_refseqs\/11_gunc\/gunc_db_progenomes2.1.dmnd",
    "ancient_dna": true
}

I ran the same code without the

--ancient_dna

and it seems to make the same contigs and bins as when I had the parameter on. So does this parameter affect downstream results, or just produce information that the user can then go through and determine if bins contain authentic aDNA?

No there is no filtering per se

Okay perfect, thank you so much!