Results

1. Studies of data structures or algorithms on PIM

• Borrows Wheeler Aligner (BWA)[pdf]
• Bloom Filters [pdf]
• Minimap2 [pdf]

2. GenoPIM library

Standard

• Bank
• Vector
• Bloom Filter
• Hash Table
• Kmers

Genomics

• DNA Banded Needelman – Wunsch
• KNN
• Sorting
• Protein Alignment
• Read Mapping

3. Application Evaluation

• Bacterial Genome Comparison
• 16S RNA Phylogeny
• DNA Consensus Sequence
• Protein Bank Search
• DNA Compression
• Short Read Mapping
• Metagenomics