Genometools

• gt-bed_to_gff3(1) Parse BED file and convert it to GFF3.
• gt-cds(1) Add CDS (coding sequence) features to exon features given in GFF3 file.
• gt-chain2dim(1) Chain pairwise matches.
• gt-chseqids(1) Change sequence ids by the mapping given in a mapping file.
• gt-clean(1) Remove all files in the current directory which are automatically created by gt.
• gt-compreads-compress(1) Generates compact encoding for fastq data.
• gt-compreads-decompress(1) Decodes a file of compressed reads.
• gt-compreads-refcompress(1) Generates compact encoding for fastq data using Reference Compressed Reads (RCR).
• gt-compreads-refdecompress(1) Decodes a given RCR (Reference Compressed Reads).
• gt-compreads(1) Call a fastq file compression tool.
• gt-condenseq(1) Call one of the CONDENSER tools to prepare or manipulate redundancy compressed genomic data.
• gt-congruence-spacedseed(1) Match spaced seeds.
• gt-congruence(1) Call a congruence subtool and pass argument(s) to it.
• gt-convertseq(1) Parse and convert sequence file formats (FASTA/FASTQ, GenBank, EMBL).
• gt-csa(1) Transform spliced alignments from GFF3 file into consensus spliced alignments.
• gt-dot(1) Prints feature graphs in dotfile format.
• gt-dupfeat(1) Duplicate internal feature nodes in given GFF3 files.
• gt-encseq-bench(1) Perform benchmark on extractions from encseq.
• gt-encseq-bitextract(1) Extracts internal data from encoded sequences.
• gt-encseq-check(1) Check the consistency of an encoded sequence file.
• gt-encseq-decode(1) Decode/extract encoded sequences.
• gt-encseq-encode(1) Encode sequence files (FASTA/FASTQ, GenBank, EMBL) efficiently.
• gt-encseq-info(1) Display meta-information about an encoded sequence.
• gt-encseq-md5(1) Display MD5 sums for an encoded sequence.
• gt-encseq-sample(1) Decode/extract encoded sequences by random choice.
• gt-encseq(1) Call an encoded sequence manipulation tool and pass argument(s) to it.
• gt-encseq2spm(1) Compute suffix prefix matches from encoded sequence.
• gt-eval(1) Compare annotation files and show accuracy measures (prediction vs. reference).
• gt-extractfeat(1) Extract features given in GFF3 file from sequence file.
• gt-extractseq(1) Extract sequences from given sequence file(s) or fastaindex.
• gt-fastq_sample(1) Print samples by random choice from given FASTQ files using at least n sequence-chars.
• gt-featureindex(1) Retrieve annotations from a persistent feature index as GFF3 output.
• gt-fingerprint(1) Compute MD5 fingerprints for each sequence given in a set of sequence files.
• gt-genomediff(1) Calculates Kr: pairwise distances between genomes.
• gt-gff3_to_gtf(1) Parse GFF3 file(s) and show them as GTF2.2.
• gt-gff3(1) Parse, possibly transform, and output GFF3 files.
• gt-gff3validator(1) Strictly validate given GFF3 files.
• gt-gtf_to_gff3(1) Parse GTF2.2 file and convert it to GFF3.
• gt-hop(1) Cognate sequence-based homopolymer error correction.
• gt-id_to_md5(1) Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences.
• gt-inlineseq_add(1) Adds inline sequences from external source to GFF3 input.
• gt-inlineseq_split(1) Split GFF3 annotations with inline sequences into separate files.
• gt-interfeat(1) Add intermediary features between outside features in given GFF3 file(s).
• gt-loccheck(1) Checks parent-child containment in GFF3 input.
• gt-ltrclustering(1) Cluster features of LTRs.
• gt-ltrdigest(1) Identifies and annotates sequence features in LTR retrotransposon candidates.
• gt-ltrharvest(1) Predict LTR retrotransposons.
• gt-matchtool(1) Parse match formats and/or invoke matching tools.
• gt-matstat(1) Compute matching statistics.
• gt-md5_to_id(1) Change MD5 fingerprints used as sequence IDs in given GFF3 files to ``regular ones.
• gt-merge(1) Merge sorted GFF3 files in sorted fashion.
• gt-mergefeat(1) Merge adjacent features without children of the same type in given GFF3 file(s).
• gt-mkfeatureindex(1) Creates a new FeatureIndex from annotation data.
• gt-mmapandread(1) Map the supplied files into memory and read them once.
• gt-orffinder(1) Identifies ORFs (open reading frames) in sequences.
• gt-packedindex(1) Call apacked index subtool and pass argument(s) to it.
• gt-prebwt(1) Precompute bwt-bounds for some prefix length.
• gt-readjoiner-assembly(1) Construct string graph and output contigs.
• gt-readjoiner-overlap(1) Compute suffix prefix matches from encoded sequence.
• gt-readjoiner-prefilter(1) Remove contained and low-quality reads and encode read set in GtEncseq format.
• gt-readjoiner(1) Readjoiner: a string graph-based sequence assembler.
• gt-repfind(1) Compute maximal exact matches (and more).
• gt-scriptfilter(1) Get info about and validate Lua script filters.
• gt-seed_extend(1) Calculate local alignments using the seed and extend algorithm.
• gt-select(1) Select certain features (specified by the used options) from given GFF3 file(s).
• gt-seq(1) Parse the given sequence file(s) and construct the corresponding index files.
• gt-seqfilter(1) Filter the given sequence file(s) and show the results on stdout.
• gt-seqids(1) Show sequence IDs from annotation file.
• gt-seqmutate(1) Mutate the sequences of the given sequence file(s).
• gt-seqorder(1) Output sequences as MultiFasta in specified order.
• gt-seqstat(1) Calculate statistics for fasta file(s).
• gt-seqtransform(1) Perform simple transformations on the given sequence file(s).
• gt-seqtranslate(1) Translates a nucleotide sequence into a protein sequence.
• gt-sequniq(1) Filter out repeated sequences in given sequence files.
• gt-shredder(1) Shredder sequence file(s) into consecutive pieces of random length.
• gt-shulengthdist(1) Compute distribution of pairwise shustring lengths.
• gt-simreads(1) Simulate sequencing reads from random positions in the input sequence(s).
• gt-sketch_page(1) Draw a multi-page PDF/PS representation of an annotation file.
• gt-sketch(1) Create graphical representation of GFF3 annotation files.
• gt-snpper(1) Annotates SNPs according to their effect on the genome as given by a genomic annotation.
• gt-speck(1) Checks spec definition compliance in GFF3 input.
• gt-splicesiteinfo(1) Show information about splice sites given in GFF3 files.
• gt-splitfasta(1) Split the supplied fasta file.
• gt-stat(1) Show statistics about features contained in GFF3 files.
• gt-tagerator(1) Map short sequence tags in given index.
• gt-tallymer-mkindex(1) Count and index k-mers in the given enhanced suffix array for a fixed value of k.
• gt-tallymer-occratio(1) Compute occurrence ratio for a set of sequences represented by an enhanced suffix array.
• gt-tallymer-search(1) Search a set of k-mers in an index constructed by ``gt tallymer mkindex.
• gt-tallymer(1) Call a tallymer subtool and pass argument(s) to it.
• gt-tirvish(1) Identify Terminal Inverted Repeat (TIR) elements,such as DNA transposons.
• gt-uniq(1) Filter out repeated feature node graphs in a sorted GFF3 file.
• gt-uniquesub(1) Compute length of minimum unique prefixes.
• gt-wtree(1) Call an wtree manipulation tool and pass argument(s) to it.
• gt(1) The GenomeTools genome analysis system.