I started my PhD in March 2015, aiming to devise and implement methods to accelerate the analysis of population resequencing data. A (frequently updated) summary of my work is here.
- kWIP, the k-mer Weighted Inner Product, which estimates genetic distance directly from NGS read sequences.
- Axe, a Trie-based sequence read demultiplexer, especially useful for GBS data.
- SeqHax is a sequence swiss army knife. SeqHax is designed to complement tools like Heng Li's seqtk with additional features for low-level sequence file manipulation (like checking that all read pairs are correctly paired, or truncating reads at a given length).