GenomeTools - Tools

# 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.