Bug#991557: ITP: broad-catch -- design sets of primers to identify genomes
Package: wnpp
Severity: wishlist
Subject: ITP: broad-catch -- design sets of primers to identify genomes
Package: wnpp
Owner: Steffen Moeller <moeller@debian.org>
Severity: wishlist
* Package name : broad-catch
Version : 1.4.0
Upstream Author : Hayden Metsky <hayden@mit.edu>
* URL : https://github.com/broadinstitute/catch
* License : MIT
Programming Lang: Python
Description : design sets of primers to identify genomes
CATCH (Compact Aggregation of Targets for Comprehensive Hybridization)
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.
Remark: This package is maintained by Debian Med Packaging Team at
https://salsa.debian.org/med-team/catch
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