Implementation and evaluation of index-based seeding strategies in SeqAn

Area

Substring Indices, read mapping, local alignment, q-mer indices

Topic

The goal of this thesis is to implement different seeding strategies using fixed length and variable length exact and approximate seeds and evaluate their runtime as well as specificity and sensitivity.

Timeline

References

  1. Kiełbasa, Szymon M, Raymond Wan, Kengo Sato, Paul Horton, and Martin C Frith. 2011. “Adaptive Seeds Tame Genomic Sequence Comparison.” Genome Research 21 (3) (March): 487–493. doi:10.1101/gr.113985.110.
  2. Horton, P, and SM Kiełbasa. 2008. “DisLex: a Transformation for Discontiguous Suffix Array Construction.” In.
  3. Kehr, B., David Weese, and Knut Reinert. 2011. “STELLAR: Fast and Exact Local Alignments.” BMC Bioinformatics 12 (Suppl 9): S15.