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Beginners
Intermediate
RNAseq
Genome Assembly
Bioinformatics
1. The Animal Farm
1.1 Animal Counting Game
1.2 Error-free Counting
2. SMRT Technology from Pacific Biosciences (PacBio)
2.1 SMRT Sequencing Method
2.2 Read Quality and Errors
2.4 Pacbio Read Simulator
2.5 File Format
2.6 HDF5 Format
3. Search and Alignment - BLASR
3.1 Statistics for Matching Seeds
3.2 How Does BLASR Work?
3.3 How To Install and Run BLASR?
4. Genome Assembly from PacBio Reads
4.1 Hybrid Assembly
4.2 HGAP
4.3 Graph-based Consensus - PBDAG-Con
4.4 HMM Consensus - Quiver
5. Error Correction of PacBio Reads using Other NGS Reads
5.1 Error Correction Using Short Reads
5.2 PacBioToCA
6. References
6.1 Bioinformatics Tools
6.2 Technology
6.3 Algorithms
6.4 Uses
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Graph-based Consensus - PBDAG-Con
We will write more on the algorithm.
