- GenomeTools has been designed to run on every POSIX compliant UNIX system. For example, Linux, Mac OS X, and OpenBSD. A Windows version which requires a Cygwin installation is available. Please report problems with it to our mailing list.
- GenomeTools publication
The GenomeTools genome analysis system is a free 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 consists of several modules.
If you are interested in gene prediction, have a look at GenomeThreader.
Platforms
G. Gremme, S. Steinbiss and S. Kurtz.
GenomeTools: a comprehensive software library for efficient processing of structured genome annotations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013, in press.
Published software in GenomeTools
The GenomeTools distribution includes several published software tools:
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ltrharvest, an efficient and flexible software tool for de novo detection of LTR retrotransposons.
D. Ellinghaus, S. Kurtz, and U. Willhoeft.
LTRharvest, a efficient and flexible software for de novo detection of LTR retrotransposons.
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tallymer, a collection of flexible and memory-efficient programs for k-mer counting and indexing of large sequence sets.
S. Kurtz, A. Narechania, J.C. Stein, and D. Ware.
A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes.
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uniquesub, a program for computing minimum unique substrings.
S. Gräf, F.G.G. Nielsen, S. Kurtz, M.A. Huynen, E. Birney, H. Stunnenberg, and P. Flicek.
Optimized design and assessment of whole genome tiling arrays.
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AnnotationSketch, a library for drawing genome annotations.
S. Steinbiss, G. Gremme, C. Schärfer, M. Mader and S. Kurtz.
AnnotationSketch: a genome annotation drawing library.
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ltrdigest, a software tool for automated annotation of internal features of LTR retrotransposons.
S. Steinbiss, U. Willhoeft, G. Gremme and S. Kurtz.
Fine-grained annotation and classification of de novo predicted LTR retrotransposons.
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MetaGenomeThreader, a software to predict genes, such as PCS's (predicted coding sequences) in sequences of metagenome projects.
D.J. Schmitz-Hübsch and S. Kurtz.
MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
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GtEncseq, a compressed biosequence representation with many features.
S. Steinbiss and S. Kurtz.
A New Efficient Data Structure for Storage and Retrieval of Multiple Biosequences.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2012, 9(2):345–357
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Readjoiner, a sequence assembler based on the assembly string graph framework.
G. Gonnella and S. Kurtz.
Readjoiner: a fast and memory efficient string graph-based sequence assembler.
The following software tools are based on the GenomeTools library:
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FISH Oracle, a web server for visualizing cancer genomics data.
M. Mader, R. Simon, S. Steinbiss and S. Kurtz.
FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context.
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ParsEval, a tool for comparing genome annotations.
D.S. Standage and V.P. Brendel.
ParsEval: parallel comparison and analysis of gene structure annotations.
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LTRsift, a graphical interface for working with LTR retrotransposon predictions.
S. Steinbiss, S. Kastens and S. Kurtz.
LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.
Contact
The GenomeTools are being developed by:
Gordon Gremme, Sascha Steinbiss, Stefan Kurtz and others
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