Mascher, Martin: POPSEQ Anchoring and ordering contig assemblies from next generation sequencing data by population sequencing. 2014
Inhalt
- Introduction
- Background
- Genetic mapping
- Meiotic recombination and genetic linkage
- Genetic markers
- Plant mapping populations
- Genetic map construction
- Next generation sequencing technologies
- Genome assembly strategies
- Methods for anchoring sequence assemblies
- The POPSEQ method
- Software used in the POPSEQ pipeline
- Barley populations and sequence data
- From FASTQ to marker-by-genotype matrix
- Framework maps
- Mapping SNPs and WGS contigs to the framework map
- Proof-of-principle of POPSEQ
- Comparison to sequenced bacterial artificial chromosomes (BACs)
- Comparison to the integrated physical and genetic map of barley
- Using different framework maps for one population
- Using different populations
- Applications of POPSEQ in genome-assisted research
- Discussion and outlook
- Impact of assembly quality and sequencing depth
- Limitations of genetic anchoring in the Triticeae
- POPSEQ for polyploid and outbred species
- Validation and improvement of the POPSEQ algorithm
- Conclusion
- Bibliography