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.