GenomeTools Tools

This list shows all GenomeTools tools and their functions.

gt The GenomeTools genome analysis system.
gt bed_to_gff3 Parse BED file and convert it to GFF3.
gt cds Add CDS (coding sequence) features to exon features given in GFF3 file.
gt chain2dim Chain pairwise matches.
gt chseqids Change sequence ids by the mapping given in a mapping file.
gt clean Remove all files in the current directory which are automatically created by gt.
gt compreads Call a fastq file compression tool.
gt compreads compress Generates compact encoding for fastq data.
gt compreads decompress Decodes a file of compressed reads.
gt compreads refcompress Generates compact encoding for fastq data using Reference Compressed Reads (RCR).
gt compreads refdecompress Decodes a given RCR (Reference Compressed Reads).
gt condenseq Call one of the CONDENSER tools to prepare or manipulate redundancy compressed genomic data.
gt congruence Call a congruence subtool and pass argument(s) to it.
gt congruence spacedseed Match spaced seeds.
gt convertseq Parse and convert sequence file formats (FASTA/FASTQ, GenBank, EMBL).
gt csa Transform spliced alignments from GFF3 file into consensus spliced alignments.
gt dot Prints feature graphs in dotfile format.
gt dupfeat Duplicate internal feature nodes in given GFF3 files.
gt encseq Call an encoded sequence manipulation tool and pass argument(s) to it.
gt encseq bench Perform benchmark on extractions from encseq.
gt encseq bitextract Extracts internal data from encoded sequences.
gt encseq check Check the consistency of an encoded sequence file.
gt encseq decode Decode/extract encoded sequences.
gt encseq encode Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.
gt encseq info Display meta-information about an encoded sequence.
gt encseq md5 Display MD5 sums for an encoded sequence.
gt encseq sample Decode/extract encoded sequences by random choice.
gt encseq2spm Compute suffix prefix matches from encoded sequence.
gt eval Compare annotation files and show accuracy measures (prediction vs. reference).
gt extractfeat Extract features given in GFF3 file from sequence file.
gt extractseq Extract sequences from given sequence file(s) or fastaindex.
gt fastq_sample Print samples by random choice from given FASTQ files using at least n sequence-chars. Output is fastq/fasta format depending on whether qualities are available.
gt featureindex Retrieve annotations from a persistent feature index as GFF3 output.
gt fingerprint Compute MD5 fingerprints for each sequence given in a set of sequence files.
gt genomediff Calculates Kr: pairwise distances between genomes.
gt gff3 Parse, possibly transform, and output GFF3 files.
gt gff3_to_gtf Parse GFF3 file(s) and show them as GTF2.2.
gt gff3validator Strictly validate given GFF3 files.
gt gtf_to_gff3 Parse GTF2.2 file and convert it to GFF3.
gt hop Cognate sequence-based homopolymer error correction.
gt id_to_md5 Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences.
gt inlineseq_add Adds inline sequences from external source to GFF3 input.
gt inlineseq_split Split GFF3 annotations with inline sequences into separate files.
gt interfeat Add intermediary features between outside features in given GFF3 file(s).
gt loccheck Checks parent-child containment in GFF3 input.
gt ltrclustering Cluster features of LTRs.
gt ltrdigest Identifies and annotates sequence features in LTR retrotransposon candidates.
gt ltrharvest Predict LTR retrotransposons.
gt matchtool Parse match formats and/or invoke matching tools.
gt matstat Compute matching statistics.
gt md5_to_id Change MD5 fingerprints used as sequence IDs in given GFF3 files to “regular” ones.
gt merge Merge sorted GFF3 files in sorted fashion.
gt mergefeat Merge adjacent features without children of the same type in given GFF3 file(s).
gt mkfeatureindex Creates a new FeatureIndex from annotation data.
gt mmapandread Map the supplied files into memory and read them once.
gt orffinder Identifies ORFs (open reading frames) in sequences.
gt packedindex Call apacked index subtool and pass argument(s) to it.
gt prebwt Precompute bwt-bounds for some prefix length.
gt readjoiner Readjoiner: a string graph-based sequence assembler.
gt readjoiner assembly Construct string graph and output contigs.
gt readjoiner overlap Compute suffix prefix matches from encoded sequence.
gt readjoiner prefilter Remove contained and low-quality reads and encode read set in GtEncseq format.
gt repfind Compute maximal exact matches (and more).
gt scriptfilter Get info about and validate Lua script filters.
gt seed_extend Calculate local alignments using the seed and extend algorithm.
gt select Select certain features (specified by the used options) from given GFF3 file(s).
gt seq Parse the given sequence file(s) and construct the corresponding index files.
gt seqfilter Filter the given sequence file(s) and show the results on stdout.
gt seqids Show sequence IDs from annotation file.
gt seqmutate Mutate the sequences of the given sequence file(s).
gt seqorder Output sequences as MultiFasta in specified order.
gt seqstat Calculate statistics for fasta file(s).
gt seqtransform Perform simple transformations on the given sequence file(s).
gt seqtranslate Translates a nucleotide sequence into a protein sequence.
gt sequniq Filter out repeated sequences in given sequence files.
gt shredder Shredder sequence file(s) into consecutive pieces of random length.
gt shulengthdist Compute distribution of pairwise shustring lengths.
gt simreads Simulate sequencing reads from random positions in the input sequence(s).
gt sketch Create graphical representation of GFF3 annotation files.
gt sketch_page Draw a multi-page PDF/PS representation of an annotation file.
gt snpper Annotates SNPs according to their effect on the genome as given by a genomic annotation.
gt speck Checks spec definition compliance in GFF3 input.
gt splicesiteinfo Show information about splice sites given in GFF3 files.
gt splitfasta Split the supplied fasta file.
gt stat Show statistics about features contained in GFF3 files.
gt tagerator Map short sequence tags in given index.
gt tallymer Call a tallymer subtool and pass argument(s) to it.
gt tallymer mkindex Count and index k-mers in the given enhanced suffix array for a fixed value of k.
gt tallymer occratio Compute occurrence ratio for a set of sequences represented by an enhanced suffix array.
gt tallymer search Search a set of k-mers in an index constructed by “gt tallymer mkindex”.
gt tirvish Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.
gt uniq Filter out repeated feature node graphs in a sorted GFF3 file.
gt uniquesub Compute length of minimum unique prefixes.
gt wtree Call an wtree manipulation tool and pass argument(s) to it.