Published March 5, 2025
| Version v1
Dataset
Open
pocpbenchmark: POCP and POCPu values and metadata tables for analysis
Authors/Creators
-
1.
Universitätsklinikum Aachen
Description
These table files for the POCP benchmark manuscript (preprint: 10.1101/2025.03.17.643616) contains POCP and POCPu values, along with genome-level and family-level metadata, plus computing metrics calculated for each nextflow processes. These very large tables are in the Parquet format and a glimpse of the content of the table is provided below.
How to read parquet files
Parquet files can be read:
- imported within R using https://nanoparquet.r-lib.org/reference/read_parquet.html
- glimpsed in a web browser:
Technical info
A glimpse at parquet files (from R function dplyr::glimpse())
pocpbenchmark_computing_metrics.parquet
Rows: 2,365,703 Columns: 9 $ Family <chr> "f__Acetobacteraceae", "f__Acetobactera… $ category <chr> "DIAMOND", "DIAMOND", "MMSEQS2", "BLAST… $ tool <chr> "DIAMOND_MAKEDB", "DIAMOND_MAKEDB", "MM… $ dataset_id <chr> "RS_GCF_017377735.1", "RS_GCF_014174155… $ realtime <chr> "1s", "0ms", "0ms", "1s", "0ms", "0ms",… $ `%cpu` <chr> "208.8%", "251.4%", "37.5%", "58.3%", "… $ peak_vmem <chr> "80.4 MB", "528.4 MB", "2 GB", "63.1 MB… $ wchar <chr> "1.6 MB", "1.6 MB", "3.4 MB", "1.9 MB",… $ rchar <chr> "1.6 MB", "1.7 MB", "3.1 MB", "1.7 MB",…
pocpbenchmark_family_metadata.parquet
Rows: 35 Columns: 7 $ Family <chr> "f__Acetobacteraceae", "f__Amphiba… $ benchmark_type <chr> "full", "full", "full", "full", "f… $ CPU_hours <dbl> 938.4, 266.3, 2080.1, 2536.2, 227.… $ n_genomes <int> 71, 34, 100, 74, 26, 77, 271, 32, … $ median_proteins <dbl> 3317.0, 3997.0, 2936.5, 5728.5, 43… $ min_proteins <dbl> 2472, 3168, 2050, 3198, 3250, 3271… $ max_proteins <dbl> 4489, 5266, 5532, 9922, 6671, 5991…
pocpbenchmark_genome_metadata.parquet
Rows: 4,767 Columns: 17 $ accession <chr> "GB_GCA_000024525.1", "GB_GCA_… $ gtdb_representative <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, … $ gtdb_taxonomy <chr> "d__Bacteria;p__Bacteroidota;c… $ Domain <chr> "d__Bacteria", "d__Bacteria", … $ Phylum <chr> "p__Bacteroidota", "p__Pseudom… $ Class <chr> "c__Bacteroidia", "c__Alphapro… $ Order <chr> "o__Cytophagales", "o__Rhodoba… $ Family <chr> "f__Spirosomaceae", "f__Rhodob… $ Genus <chr> "g__Spirosoma", "g__Ruegeria",… $ Species <chr> "s__Spirosoma linguale", "s__R… $ family <chr> "f__Spirosomaceae", "f__Rhodob… $ num_seqs <dbl> 7129, 3495, 3414, 3208, 2149, … $ sum_len <dbl> 2497095, 1057624, 649075, 9969… $ min_len <dbl> 30, 30, 20, 21, 30, 30, 20, 22… $ avg_len <dbl> 350.3, 302.6, 190.1, 310.8, 28… $ max_len <dbl> 5545, 1511, 1221, 3965, 7961, … $ genome_size <dbl> 8491258, 3523710, 2298088, 341…
pocpbenchmark_pocp_values.parquet
Rows: 2,358,466 Columns: 16 $ type <chr> "POCP", "POCPu", "POCP", "PO… $ tool <fct> BLAST_BLASTP, BLAST_BLASTP, … $ is_recommended_tool <lgl> FALSE, FALSE, FALSE, FALSE, … $ pocp <dbl> 80.77531, 61.63676, 80.77531… $ query <chr> "RS_GCF_000021325.1", "RS_GC… $ subject <chr> "RS_GCF_000182745.2", "RS_GC… $ query_genus <chr> "g__Gluconacetobacter", "g__… $ query_gtdb_taxonomy <chr> "d__Bacteria;p__Pseudomonado… $ subject_genus <chr> "g__Komagataeibacter", "g__K… $ subject_gtdb_taxonomy <chr> "d__Bacteria;p__Pseudomonado… $ same_genus_truth <lgl> FALSE, FALSE, FALSE, FALSE, … $ same_genus <lgl> TRUE, TRUE, TRUE, TRUE, TRUE… $ class <chr> "FP", "FP", "FP", "FP", "FP"… $ same_genus_random <lgl> FALSE, TRUE, TRUE, TRUE, FAL… $ class_random <chr> "TN", "FP", "FP", "FP", "TN"… $ Family <chr> "f__Acetobacteraceae", "f__A…
Files
Additional details
Related works
- Continues
- Dataset: 10.5281/zenodo.14974869 (DOI)
- Is derived from
- Workflow: https://github.com/ClavelLab/pocpbenchmark_manuscript/blob/0b1f0e0e96f871d02f5c18f274d34b974224bcb4/targets_prepare_pocpbenchmark_data.R (URL)
- Is published in
- Preprint: 10.1101/2025.03.17.643616 (DOI)
- Journal article: 10.7717/peerj.20259 (DOI)
- Is required by
- Workflow: https://github.com/ClavelLab/pocpbenchmark_manuscript/blob/0b1f0e0e96f871d02f5c18f274d34b974224bcb4/targets_analyze_pocpbenchmark_data.R (URL)
References
- Pauvert C, Hitch TCA, Clavel T. 2025. Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu) PeerJ 13:e20259 https://doi.org/10.7717/peerj.20259