Bremges, Andreas: Assembling the microbial dark matter. 2016
Inhalt
- I GENOMES FROM SINGLE CELLS
- The cutting edge of single cell assembly
- Reference single amplified genomes
- Assessment of single cell assemblers
- Evolution of the SPAdes assembler
- Conclusions
- Metagenome-enabled error correction
- Cartoonesque k-mer relationship
- Error correction algorithm
- Reference SAGs and mock metagenome
- Performance of SAG error correction
- Effect on SAG assembly
- Metagenome coverage threshold
- Conclusions
- Software availability
- Metagenomic proxy assemblies
- Metagenomic proxy reads
- The choice of k
- Precision and recall
- On-the-fly recruitment seed expansion
- Contaminating or decontaminating?
- Assembling metagenomic proxy reads
- Aminacenantes (OP8) single cells from Sakinaw Lake
- Aminacenantes (OP8) metagenomic proxy assemblies
- Conclusions
- Implementation details
- Software availability
- An integrated assembly pipeline
- II GENOMES FROM METAGENOMES
- Metagenome assembly and binning techniques
- Assembling a biogas-producing community
- Digester management and process characterization
- Sampling and library construction
- Metagenomic and metatranscriptomic sequencing
- Read quality control
- Metagenome assembly and annotation
- Relating the metagenome and the metatranscriptome
- In retrospect: Metagenome binning
- Conclusions
- A genome catalog of the biogas microbiome
- Metagenome sampling and sequencing
- Community structure and similarity
- Combined metagenome assembly
- Metagenome binning
- Abundant distinct taxa
- Conclusions
- Setting the stage for future biogas research
- Epilogue: The CAMI initiative