iKISS Output

This is a overwiew of iKISS output directory:

OUTPUT-KISS/
   config_corrected.yaml
   0.FASTQ_STATS
   └── fastq_stats.txt
   1.KMERS_MODULE
   ├── Clone12
   ├── Clone14
   ├── Clone16
   ├── Clone2
   ├── Clone20
   ├── Clone4
   └── Clone8
   2.KMERS_TABLE
   ├── kmers_list_paths.txt
   ├── kmers_table.names
   ├── kmers_table.table
   ├── kmers_to_use
   ├── kmers_to_use.no_pass_kmers
   ├── kmers_to_use.shareness
   ├── kmers_to_use.stats.both
   ├── kmers_to_use.stats.only_canonical
   └── kmers_to_use.stats.only_non_canonical
   3.TABLE2BED
   ├── log
   ├── output_file.0.bed
   ├── output_file.0.bim
   ├── output_file.0.fam
   ├── output_file.1.bed
   ├── output_file.1.bim
   ├── output_file.1.fam
   ├── output_file.2.bed
   ├── output_file.2.bim
   ├── output_file.2.fam
   ├── output_file.3.bed
   ├── output_file.3.bim
   ├── output_file.3.fam
   ├── output_file.4.bed
   ├── output_file.4.bim
   └── output_file.4.fam
   4.EXTRACT_FASTA
   ├── output_file.0.fasta.gz
   ├── output_file.1.fasta.gz
   ├── output_file.2.fasta.gz
   ├── output_file.3.fasta.gz
   └── output_file.4.fasta.gz
   5.RANGES
   ├── output_file.0
   ├── output_file.1
   ├── output_file.2
   ├── output_file.3
   └── output_file.4
   6.LFMM
   ├── output_file.0_10_LFMM_outliers.csv
   ├── output_file.0_10_LFMM_pvalues.csv
   ├── output_file.0_10_LFMM.rplot.pdf
   ...
   6.LFMM_PHENO
   ├── PCA_from_phenotype.csv
   ├── PCA_from_phenotype.html
   └── PCA_from_phenotype.ipynb
   6.PCADAPT
   ├── output_file.0_10_PCADAPT_outliers.csv
   ├── output_file.0_10_PCADAPT_pvalues.csv
   ├── output_file.0_10_PCADAPT.rplot.pdf
   ├── output_file.0_10_PCADAPT_scores.csv
   6.SNMF
   ├── output_file.0_5_SNMF/
   ├── output_file.0_2_SNMF/
      ├── kmer.geno
      ├── kmer.snmf/
         ├── K2
             ├── run1
             ├── run2
             ├── run3
         ├── K3
      ├── kmer.snmf.pdf
      ├── kmer.snmfProject
   ...
   7.MERGED_LFMM
   ├── merged_LFMM_outliers.csv
   └── merged_LFMM_pvalues.csv
   7.MERGED_PCADAPT
   ├── merged_PCADAPT_outliers.csv
   └── merged_PCADAPT_pvalues.csv
   8.MAPPING_KMERS
   ├── bam_files.txt
   ├── output_file.0_vs_reference.bam
   ├── output_file.0_vs_reference_FMQ.bam
   ├── output_file.0_vs_reference.sai
   ├── output_file.0_vs_reference_sorted.bam
   ├── output_file.0_vs_reference_sorted.bam.bai
   ├── output_file.0_vs_reference_sorted.bam.idxstats
   ├── output_file.0_vs_reference_sorted.bam.stats
   ...
   9.KMERPOSITION
   ├── output_file.0_vs_reference_KMERPOSITION.txt
   ├── output_file.1_vs_reference_KMERPOSITION.txt
   ├── output_file.2_vs_reference_KMERPOSITION.txt
   ├── output_file.3_vs_reference_KMERPOSITION.txt
   └── output_file.4_vs_reference_KMERPOSITION.txt
   10.MERGE_KMERPOSITION
   ├── kmer_position_merged.txt
   └── kmer_position_samtools_merge.bam
   11.OUTLIERS_LFMM_POSITION
   └── outliers_with_position.csv
   11.OUTLIERS_PCADAPT_POSITION
   └── outliers_with_position.csv
   12.ASSEMBLY_OUTLIERS_LFMM
   ├── contigs_LFMM_vs_reference.bam
   ├── contigs_LFMM_vs_reference.sorted.bam
   ├── contigs_LFMM_vs_reference.sorted.bam.bai
   ├── contigs_LFMM_vs_reference.sorted.bam.idxstats
   ├── contigs_LFMM_vs_reference.sorted.bam.stats
   ├── outliers_LFMM_mergetags.csv
   └── outliers_LFMM_mergetags.fasta
   12.ASSEMBLY_OUTLIERS_PCADAPT
   ├── contigs_PCADAPT_vs_reference.bam
   ├── contigs_PCADAPT_vs_reference.sorted.bam
   ├── contigs_PCADAPT_vs_reference.sorted.bam.bai
   ├── contigs_PCADAPT_vs_reference.sorted.bam.idxstats
   ├── contigs_PCADAPT_vs_reference.sorted.bam.stats
   ├── outliers_PCADAPT_mergetags.csv
   └── outliers_PCADAPT_mergetags.fasta
   13.GFF_FEATURES
   └── extracted.gff
   14.CONTIGS_INTERSECT_LFMM
   └── contigs_intersect_annotation.bed
   14.CONTIGS_INTERSECT_PCADAPT
   └── contigs_intersect_annotation.bed
   14.KMERS_INTERSECT
   └── kmers_bedtools_intersect_annotation.bed
   15.STATS_INTERSECT
    ├── ALLKMERS_INTERSECT
    │   └── intersect_stats
    │       ├── nb_feature_by_chr.csv
    │       ├── nb_feature_by_gene.csv
    │       └── nb_feature_by_gene_filter.csv
    ├── CONTIGS_LFMM_INTERSECT
    ├── CONTIGS_PCADAPT_INTERSECT
    ├── OUTLIERS_LFMM_INTERSECT
    └── OUTLIERS_PCADAPT_INTERSECT
  16.KMERS_IN_GENES_MATRIX
    ├── global_presence_absence_matrix.txt
    ├── kmers_into_feature.fasta
  17.MATRIX_AND_ANNOTATION
    ├── annotations_and_binary_matrix_info.csv
    ├── occurrences_by_group.csv
    └── occurrences_by_sample.csv
   REF
   ├── reference2.fasta
   ├── reference2.fasta.0123
   ├── reference2.fasta.amb
   ├── reference2.fasta.ann
   ├── reference2.fasta.bwt.2bit.64
   ├── reference2.fasta.pac
   ├── reference.fasta
   ├── reference.fasta.amb
   ├── reference.fasta.ann
   ├── reference.fasta.bwt
   ├── reference.fasta.pac
   └── reference.fasta.sa
   REPORT
   ├── iKISS_report.csv
   ├── iKISS_report.html
   ├── iKISS_report.ipynb
   ├── PCA_from_phenotype.html
   └── PCA_from_phenotype.ipynb
   BENCHMARK
   LOGS

Note

We recommended to remove 1.KMER_GWAS repertory after analysis.