Catch¶
Description¶
Compact Aggregation of Targets for Comprehensive Hybridization CATCH is a Python package for designing probe sets to use for nucleic acid capture of diverse sequence. Comprehensive coverage: CATCH accepts any collection of unaligned sequences — typically whole genomes of all known genetic diversity of one or more microbial species. It designs oligo sequences that guarantee coverage of this diversity, enabling rapid design of exhaustive probe sets for customizable targets. Compact designs: CATCH can design with a specified constraint on the number of oligos (e.g., array size). It searches a space of probe sets, which may pool many species, to find an optimal design. This allows its designs to scale well with known genetic diversity, and also supports cost-effective applications. Flexibility: CATCH supports applications beyond whole genome enrichment, such as differential identification of species. It allows blacklisting sequence from the design (e.g., background in microbial enrichment), supports customized models of hybridization, enables weighting the sensitivity for different species, and more.
Environment Modules¶
Run module spider catch to find out what environment modules are available for this application.
Environment Variables¶
- HPC_CATCH_DIR - installation directory
- HPC_CATCH_BIN - executable directory
Citation¶
If you publish research that uses Catch you have to cite it as follows:
Metsky HC and Siddle KJ et al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nature Biotechnology, 37(2), 160–168 (2019). doi: 10.1038/s41587-018-0006-x
Categories¶
biology, genomics, sequencing