The GenomeTools genome analysis system is a collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt.
It is based on a C library named libgenometools which contains a wide variety of classes for efficient and convenient implementation of sequence and annotation processing software.
GenomeTools has been designed to run on every POSIX compliant UNIX system — for example Linux or macOS. A reduced Windows version is also available.
This is free and open source software.
Some of the tools are:
- LTRharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
- Tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
- uniquesub, a program for computing minimum unique substrings.
- AnnotationSketch, a library for drawing genome annotations.
- LTRdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
- MetaGenomeThreader, a software to predict genes, such as PCS’s (predicted coding sequences) in sequences of metagenome projects.
- GtEncseq, a compressed biosequence representation with many features.
- Readjoiner, a sequence assembler based on the assembly string graph framework.
Website: genometools.org
Support: GitHub Code Repository
Developer: Broad Institute, Inc.
License: Apache License 2.0
GenomeTools is written in C. Learn C with our recommended free books and free tutorials.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
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