DOI: 10.5281/zenodo.14975029
title: pocpbenchmark: POCP and POCPu values and metadata tables for analysis

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:



https://parquetreader.com

https://www.parquet-viewer.com/
description: A glimpse at parquet files (from R function dplyr::glimpse())pocpbenchmark_computing_metrics.parquetRows: 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.parquetRows: 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.parquetRows: 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.parquetRows: 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…