Outputs

Depending on the parameters, kmtricks can produce several different outputs. Below is an exhaustive example of all kind of files that can be produced with 2 samples as inputs, D1 and D2 (only the first partition is shown, partition_0).

kmtricks_dir
├── build_infos.txt   # informations about kmtricks compilation
├── options.txt       # User parameters
├── run_infos.txt     # Execution time and peak memory
├── config_gatb       # Configuration storage
│   └── gatb.config
├── counts            # Counts storage
│   └── partition_0
│       ├── D1.hash   # counted hashes file
│       ├── D1.kmer   # counted k-mers file
│       ├── D1.kff    # counted k-mers in kff format
│       ├── D1.vector # hashes represented by a bit-vector
│       ├── D2.hash
│       ├── D2.kmer
│       ├── D2.kff
│       └── D2.vector
├── partition_infos   # Partition infos storage, each file contains the number of k-mers in each partitions
│   ├── D1.pinfo    
│   └── D2.pinfo
├── filters           # Bloom filters storage
│   ├── D1.sdsl       # Bloom filter in sdsl format
│   ├── D2.sdsl
│   ├── D1.bf         # Bloom filter in HowDeSBT format
│   └── D2.bf
├── hash.info         # partition hashing info
├── histograms        # histogram storage
│   ├── D1.hist       # k-mer histogram file
│   └── D2.hist
├── howde_index       # HowDeSBT index storage
├── kmtricks.fof      # copy of kmtricks input file
├── matrices          # Matrices storage
│   ├── matrix_0.cmbf            # Bloom filter matrix (column-major)
│   ├── matrix_0.count           # Counted k-mers matrix
│   ├── matrix_0.count_hash      # Counted hashes matrix
│   ├── matrix_0.count_hash.txt  # Counted hashes matrix (human readable)
│   ├── matrix_0.count.txt       # Counted k-mers matrix (human readable)
│   ├── matrix_0.pa              # Presence/absence k-mers matrix
│   ├── matrix_0.pa_hash         # Presence/absence hashes matrix
│   ├── matrix_0.pa_hash.txt     # Presence/absence hashes matrix (human readable)
│   ├── matrix_0.pa.txt          # Presence/absence k-mers matrix (human readable)
│   └── matrix_0.rmbf            # Bloom filter matrix (row-major)
├── minimizers
│   └── minimizers.0             # Minimizers of partition 0, sorted text format
├── merge_infos                  # merge statistics storage
│   └── partition0.merge_info    
├── repartition_gatb             # minimizer repartition
│   └── repartition.minimRepart
└── superkmers                   # super-k-mers storage
    ├── D1
    │   ├── PartiInfoFile        # Partition infos
    │   ├── skp.0                # Super-k-mers from partition 0
    │   └── SuperKmerBinInfoFile
    └── D2
        ├── PartiInfoFile
        ├── skp.0
        └── SuperKmerBinInfoFile

See also : kmtricks dump, kmtricks aggregate and kmtricks API