Abstract
BACKGROUND: Traditional Map based Cloning approaches, used for the identification of desirable alleles, are extremely labour intensive and years can elapse between the mutagenesis and the detection of the polymorphism. High throughput sequencing based Mapping-by-sequencing approach requires an ordered genome assembly and cannot be used with fragmented, un-scaffolded draft genomes, limiting its application to model species and precluding many important organisms. RESULTS: We addressed this gap in resource and presented a computational method and software implementations called CHERIPIC (Computing Homozygosity Enriched Regions In genomes to Prioritise Identification of Candidate variants). We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively. CONCLUSIONS: CHERIPIC allows users to rapidly analyse bulk segregant sequence data and we have made it available as a pre-packaged binary with all dependencies for Linux and MacOS and as Galaxy tool.
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Claims 4
Claim · model-written summary
CHERIPIC was successfully validated on Arabidopsis bulk segregant sequence data.
- Taxon
- Arabidopsis
Arabidopsise0 - Outcome
- successfully validated implementation of CHERIPICe0
- Comparator
- three different types of bulk segregant sequence datae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively.”
Claim · model-written summary
CHERIPIC was successfully validated on maize bulk segregant sequence data.
- Outcome
- successfully validated implementation of CHERIPICe0
- Comparator
- three different types of bulk segregant sequence datae0
Zea maysOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively.”
Claim · model-written summary
CHERIPIC was successfully validated on barley bulk segregant sequence data.
- Taxon
- barley
.jpg?width=60)
Hordeum vulgaree0 - Outcome
- successfully validated implementation of CHERIPICe0
- Comparator
- three different types of bulk segregant sequence datae0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
.jpg?width=500)
Verbatim
e0“We have successfully validated implementation of CHERIPIC using three different types of bulk segregant sequence data from Arabidopsis, maize and barley, respectively.”
Claim · model-written summary
CHERIPIC was released as a binary for Linux and MacOS and as a Galaxy tool.
Verbatim
e0“we have made it available as a pre-packaged binary with all dependencies for Linux and MacOS and as Galaxy tool.”
e1“CHERIPIC allows users to rapidly analyse bulk segregant sequence data”