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TOOLS
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antibody-sequences-finder tools.AntibodyFinderMain Antibody sequences finder in De Bruijn graph
bin2fasta tools.BinaryToFasta Converts different binary objects to FASTA format
comp2graph tools.ComponentsToGraph Transforms components in binary format to de Bruijn graph in GFA format
comp2seq tools.ComponentsToSequences Transforms components in binary format to FASTA sequences (contigs)
comparison-script tools.CompareReadsAndComponentsMain Statistics
component-colored tools.ColoredComponentMain Extract graph components from tangled graph based on k-mers coloring
component-cutter tools.ComponentCutterMain Build graph components from tangled graph
component-extractor tools.ComponentExtractorMain Extract graph components from tangled graph based on pivot k-mers
component-paths tools.ComponentPathsMain Extracts paths in the components
dist-matrix-calculator tools.DistanceMatrixCalculatorMain Calculates distance matrix using features values
double-view tools.DoubleViewMain Converts two binary k-mers files to single text file
features-calculator tools.FeaturesCalculatorMain Calculates features values for input reads files
heatmap-maker tools.HeatMapMakerMain constructs heatmap with dendrogram for distance matrix
kmer-counter tools.KmersCounterMain Count k-mers in given reads with ArrayLong2IntHashMap
kmer-counter-many tools.KmersCounterForManyFilesMain Count k-mers for many files independently
kmer-counter-posneg tools.KmersCounterPositiveNegative Count k-mers for files from two groups independently
kmers-color tools.ColorKmersMain Color k-mers based on occurrences in classes
kmers-filter tools.KmersFilter Filter k-mers from test set according to known samples
kmers-grouped-counter tools.KmersGroupedSamplesCounter Count number of samples from 3 groups containing specified k-mers
kmers-multiple-filters tools.KmersMultipleFilters Filter k-mers from test set according to three specified sets
kmers-per-sample tools.KmersPerSampleCounter Counts the abundance of frequent k-mers from dataset in each sample
kmers-samples-counter tools.KmersSamplesCounter Count number of samples containing k-mers from multiple samples
matrix-builder tools.DistanceMatrixBuilderMain Builds the distance matrix for input sequences
seq-builder tools.SeqBuilderMain Metagenome De Bruijn graph analysis and sequences building
seq-builder-many tools.SeqBuilderForManyFilesMain Metagenome De Bruijn graph analysis and sequences building for many files independently
seq2comp tools.SequencesToComponents Transforms sequences to components
specific-kmers tools.SpecificKmersFinder Output k-mers specific to groups of samples based on chi-squared & Mann-Whitney tests
specific-kmers-3 tools.SpecificKmers3GroupsFinder Output k-mers specific to each of three groups of samples based on chi-squared & Mann-Whitney tests
stats-features tools.StatsFeaturesBuilderMain Builds statistically significant features for group of metagenomic samples
stats-kmers tools.StatsKmersFinder Output k-mers statistically significant to each of two groups of samples based on chi-squared & Mann-Whitney test
stats-kmers-3 tools.StatsKmers3GroupsFinder Output k-mers statistically significant to each of three groups of samples based on chi-squared & Mann-Whitney test
subset-specific tools.SubsetSpecificExtractor Output subset of top most specific k-mers based on given statistical ranking
supergraph-sequence-builder tools.SupergraphSeqBuilderMain NOT COMPLETED
top-stats-kmers tools.TopStatsKmersFinder Output specified number of best (by p-value) k-mers based on chi-squared test
unique-features tools.UniqueFeaturesBuilderMain Builds unique features for group of metagenomic samples
unique-kmers tools.UniqueKmersFinder Output k-mers present in one dataset and missing in other
unique-kmers-multi tools.UniqueKmersMultipleSamplesFinder Output k-mers present in one dataset in fixed number of samples and missing in other
view tools.ViewMain Converts different binary objects to text format