gt

Initialize gt for the repository in the current directory

$ gt init

$ gt create [branch_name]

$ gt modify -cam [commit_message]

$ gt stack submit

$ gt co [branch_name]

$ gt sync

$ gt log short

$ gt [subcommand] --help

gt [GLOBAL_OPTIONS] <TOOL> [TOOL_OPTIONS] [ARGUMENTS]

Examples:
gt gff3 -tidy annotations.gff3
gt stat genome.fa
gt seq -showfasta -o output.fa input.fastq

-help, -h
    Displays a help message for the gt command or the specified tool.

-version
    Shows the version information of the GenomeTools suite.

-memlimit [bytes]
    Sets a limit on the total memory that can be allocated by gt processes.

-cpulimit [seconds]
    Sets a limit on the CPU time (in seconds) that can be used by gt processes.

-force
    Forces overwriting of existing output files without prompting.

-verbose
    Increases the verbosity of output messages, providing more detailed information during execution.

-warning
    Activates warning messages, which are typically suppressed by default.

-debug
    Enables debugging output, useful for developers and advanced troubleshooting.

-output [filename]
    Redirects standard output to the specified file instead of the console.

-log [filename]
    Redirects log messages to the specified file.

Note: 'gt' is not a standard, universally available Linux command. This analysis refers to 'gt' as provided by the GenomeTools suite, a specialized toolkit for bioinformatics and genomics.

The gt (GenomeTools) command serves as the central entry point for a comprehensive open-source software system designed for genome analysis. It offers a rich collection of tools and libraries for processing genomic sequences, annotations (such as GFF3 and GTF formats), and alignment data. Its core functionalities include parsing, validating, and transforming common genome annotation formats, performing diverse sequence manipulations, building efficient data structures like suffix arrays, and providing a robust framework for developing custom bioinformatics applications. gt is widely utilized in genomics research for tasks ranging from fundamental sequence operations to more intricate comparative genomics and annotation processing workflows.

The gt command, as part of GenomeTools, is not installed by default on most Linux distributions. It requires separate installation, typically from source, a package manager (e.g., `apt install genometools-dev`), or through bioinformatics-specific environment managers like Conda. Its extensive functionality is highly specialized for bioinformatics and genomics tasks, making it less relevant for general system administration or common command-line operations. Many of its subcommands can be computationally intensive, requiring significant memory and CPU resources for large genomic datasets.

The gt command functions as a dispatcher, invoking a wide array of specialized tools. Each tool (``) addresses a specific genomic analysis task and has its own set of options. Here are a few frequently used subcommands:

gt gff3: A versatile tool for manipulating, validating, and transforming GFF3 (General Feature Format, version 3) annotation files. It can check for syntax errors, canonicalize entries, and perform various filtering operations.

gt stat: Used to compute comprehensive statistics on genomic sequence files (FASTA/FASTQ) or annotation files (GFF3/GTF), providing insights into their content and structure.

gt seq: Provides functionalities for operating on sequence files, such as concatenating, reversing, complementing, and extracting subsequences, as well as converting between FASTA and FASTQ formats.

gt extractfeat: Extracts annotated features (e.g., genes, CDS, exons) from genomic sequences based on the information provided in GFF3/GTF annotation files.

gt suffixerator: A core tool for constructing advanced data structures like suffix arrays, enhanced suffix arrays (ESA), and suffix trees, which are fundamental for efficient string matching and sequence analysis algorithms.

The GenomeTools project originated at the Center for Biotechnology (CeBiTec) at Bielefeld University in Germany. Its development began with a focus on efficient data structures for sequence analysis, particularly the implementation and application of suffix arrays. Over the years, it evolved into a comprehensive and modular software suite, driven by the increasing need for robust and standardized tools in genomics research. A significant emphasis has been placed on supporting standard file formats like GFF3 and GTF, ensuring interoperability within the bioinformatics ecosystem. Its development continues to be an ongoing, community-driven effort, adapting to the evolving challenges and demands of modern genomics.

samtools(1), bedtools(1), bowtie2(1), bwa(1), grep(1), awk(1)