TOPAS - TOolkit for Processing and Annotating Sequence data
This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules.
Example Invocation:
java -jar topas.jar -?
This lists all available modules.
FASTA Processing Modules
FASTQ Processing Modules
GFF Processing Modules
VCF Processing Modules
Validate FASTA
Validate FASTQ
Validate GFF3
Index VCF
Correct FASTA
Format FASTQ
Sort GFF3
Filter VCF
Index FASTA
Filter GFF3
Annotate VCF
Extract FASTA
Analyse VCF
Tabulate FASTA
GenConS
VCF Processing Modules
GenConS - Generate Consensus Sequence
GenConS reads a FASTA reference and a corresponding GATK Unified Genotyper VCF file of which a consensus sequence is created. The key feature of this module is that it is able to handle ancient DNA data. For instance, the user can set the expected DNA damage individually. This is reflected in the resulting consensus sequence. For a detailed description of the tool see the wiki page https://github.com/subwaystation/TOPAS/wiki#gencons. The GenConS module has been applied to aDNA data of mammoths! For further details see https://doi.org/10.1038/s41598-017-17723-1.
TOPAS - TOolkit for Processing and Annotating Sequence data
This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The
FASTAprocessing modules, theFASTQprocessing modules, theGFFprocessing modules and theVCFprocessing modules.Example Invocation:
java -jar topas.jar -?This lists all available modules.VCF Processing Modules
GenConS - Generate Consensus Sequence
GenConS reads a FASTA reference and a corresponding GATK Unified Genotyper VCF file of which a consensus sequence is created. The key feature of this module is that it is able to handle ancient DNA data. For instance, the user can set the expected DNA damage individually. This is reflected in the resulting consensus sequence. For a detailed description of the tool see the wiki page https://github.com/subwaystation/TOPAS/wiki#gencons.
The GenConS module has been applied to aDNA data of mammoths! For further details see https://doi.org/10.1038/s41598-017-17723-1.
For a more detailed insight (except the GenConS module) see https://github.com/subwaystation/TOPAS/blob/master/BSC_Thesis_Heumos.pdf
LICENSE
TOPAS is available free of charge for academic purposes. The toolkit is available under the CC-BY license.