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 |
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
TOPAS is available free of charge for academic purposes. The toolkit is available under the CC-BY license.