Raw inputs from jupyter lab scripts. Some inputs were preprocessed to be easily exported here and may not directly reflect software output.
Kraken/Bracken:
- bracken_self_combine_result.tsv.gz: Concatenated bracken report of Illumina reads against a single database composed of SPMP SLCs.
- bracken_western_combine_result.tsv.gz: Bracken result of western reads against SPMP dataset
- cre_classified.tsv: Percentage of reads classified by kraken for each CRE sample against various database
- kraken_self_single_results.tsv.gz: Concatenated kraken reports of Illumina reads against short-read and hybrid assemblies.
- kraken_standard_all.parquet.tsv.gz: Concatenated kraken reports of Illumina reads against the Kraken Standard database (saved in parquet format).
Reads data:
- illumina_reads_statistics.tsv.gz: Illumina reads statistics data
- nanopore_reads_statistics.tsv.gz: ONT reads statistics data
- illumina_nanopore_reads_correlation.tsv.gz: Illumina and ONT reads mapping against the kraken standard database, used for reads correlation
GTDB:
- gtdb_mash_distances.tsv.gz: Mash distance between Hybrid assemblies and GTDB genomes
- gtdb_metadata.tsv.gz: GTDB genomes metadata
Mags info:
- mags_info_hybrid.tsv: Hybrid MAGs assembly statistics and annotations. Only MAGs of medium, near-complete and high quality were conserved.
- mags_info_shortread.tsv: Short-read MAGs assembly statistics and annotations. Only MAGs of medium, near-complete and high quality were conserved.
- mags_info_hic.tsv: HiC MAGs assembly statistics
Strains clustering:
- strains_clustering_results.tsv.gz: All MASH strains clustering results
- 280.fastani.tsv.gz: Pairwise FastANI distances of SLC280 strains
Other metadata:
- subjects_metadata.tsv: SPMP subject metadata
- uhgg-genomes-all_metadata.tsv.gz: UHGG all genomes metadata
BGC:
- all_GCF_curated_metadata.tsv: Metadata for each BGC not encoding an unknown product. Includes important information including which predicted product classes and which GCF they belong to.
- final_rep_clusters.tsv: Metadata for representative clusters for each unique Gene Cluster Family (GCF)
- bgc_novel_bact_corr_edge_bins.tsv: Correlation subset values used for bacteriocin network (with transporter)
- bgc_bact_no_trans_corr_edge_bins.tsv: Correlation subset values used for bacteriocin network (without transporter)
Anti-microbial/anti-bacterial peptide prediction:
- ampgram_benchmark_CHOSEN.fasta: Multi-fasta file containing 78 validated anti-microbial/anti-bacterial peptides (AMP/ABPs) and 78 scrambled negative control sequences for benchmarking
- ampgram_benchmark_CHOSEN.fastaheaders: Tab separated file with the names of each peptide in the benchmarking dataset
- AMPDiscover_benchmark_predictions.csv: AMPDiscover prediction results for the benchmarking peptide sequences.
- ampgram_benchmark_df.tsv: AmpGram prediction results for the benchmarking peptide sequences
- ampscannerv2_benchmark_Prediction_Summary.csv: AMPScanner v2 prediction results for the benchmarking peptide sequences
- all_AS_novel_peptides.sizes: AA lengths of every short ORF > 10 AA and < 200 AA in novel BGCs encoding peptides with transporters, after Antismash predictions.
- AS_peptides_with_transporter_gene_funcs_combined.tsv: Antismash annotated gene functions for every short ORF hort ORF > 10 AA and < 200 AA in novel BGCs encoding peptides with transporters
- AS_novel_peptide_transporter_AMPDiscover_predictions.csv: AMPDiscover prediction results for candidate peptide sequences in BGCs with transporters this manuscript.
- all_AS_novel_peptides_ampgram.tsv: AmpGram prediction results for candidate peptide sequences in BGCs with transporters in this manuscript.
- AS_novel_peptides_Prediction_Summary.csv: AMPScanner v2 prediction results for candidate peptide sequences in BGCs with transporters in this manuscript.