Man Pages in genometools

Section 1: Executable programs or shell commands

gt.1

The genometools genome analysis system.

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.1

Call a fastq file compression tool.

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-condenser.1

Call one of the condenser tools to prepare or manipulate redundancie compressed genomic data.

gt-congruence.1

Call a congruence subtool and pass argument(s) to it.

gt-congruence-spacedseed.1

Match spaced seeds.

gt-convertseq.1

Parse and convert sequence file formats.

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.1

Call an encoded sequence manipulation tool and pass argument(s) to it.

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 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-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. output is fastq/fasta format depending on whether qualities are available.

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-gff3.1

Parse, possibly transform, and output gff3 files.

gt-gff3_to_gtf.1

Parse gff3 file(s) and show them as gtf2.2.

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-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.1

Readjoiner: a string graph-based sequence assembler.

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-repfind.1

Compute maximal repeats.

gt-scriptfilter.1

Get info about and validate lua script filters.

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.1

Create graphical representation of gff3 annotation files.

gt-sketch_page.1

Draw a multi-page pdf/ps representation of an annotation file.

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.1

Call a tallymer subtool and pass argument(s) to it.

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-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.