K-mer classification method improvement
New k-mer classification method with improved scaling
The output file names and locations have been changed for some functionalities (Sorry DJ).
kmer_classification
-
kmer_distance_tree.R -> genome_kmer_distance_tree.R
-
distance_inf_distinct_kmers.csv -> removed
-
mash_distance.csv -> distances_for_tree/genome_mash_distance.csv
-
distance_distinct_kmers.csv -> distances_for_tree/genome_distance_distinct_kmers.csv
-
distance_all_kmers.csv -> distances_for_tree/genome_distance_all_kmers.csv
-
core_kmers.csv -> kmer_identifiers/core_kmers.csv
-
accessory_kmers.csv -> kmer_identifiers/accessory_kmers.csv
-
unique_kmers.csv -> kmer_identifiers/unique_kmers.csv
-
phenotype_shared_kmers.csv -> kmer_identifiers/phenotype_shared_kmers.csv
-
phenotype_specific_kmers.csv -> kmer_identifiers/phenotype_specific_kmers.csv
-
phenotype_exclusive_kmers.csv -> kmer_identifiers/phenotype_exclusive_kmers.csv
function_overview
- function_overview_per_group.csv -> removed
- go_overview.txt -> go_overview.csv
- pfam_overview.txt -> pfam_overview.csv
- tigrfam_overview.txt -> tigrfam_overview.csv
- interpro_overview.txt -> interpro_overview.csv
- bgc_overview.txt -> bgc_overview.csv
- phobius_overview.txt -> phobius_signalp_overview.txt
- cog_overview.txt -> cog_overview.csv
rename_phylogeny
- tree.newick_RENAMED -> tree_RENAMED.newick
msa_of_group
- informative/variable_sites.csv -> informative/variable_site_counts.csv
calculate_ANI
- ani.tree -> ANI.newick