Bioinformatics software -- the programs are also available on GitHub: https://github.com/lucian-ilie
Error correction in DNA sequencing data
- Correcting Illumina Data
- New methods and tools for thorough evaluation of error correcting performance
- M. Molnar, L. Ilie, Correcting Illumina data, Briefings in Bioinformatics (2014), bbu029.
- RACER: Rapid and Accurate Correction of Errors in Reads
- Accurate and efficient correction of errors in NGS data
- L. Ilie, M. Molnar, RACER: Rapid and Accurate Correction of Errors in Reads, Bioinformatics 29 (2013) 2490 -- 2493.
- HiTEC: High-Throughput Error Correction
- Accurate error correction in NGS data
- L. Ilie, F. Fazayeli, and S. Ilie, HiTEC: accurate error correction in high-throughput sequencing data, Bioinformatics 27(3) (2011) 295 -- 302.
Sequence similarity search
DNA Oligonucleotide design
Short read mapping
- SHRiMP: Short Read Mapping Program
- Accurate mapping of short color-space reads
- SHRiMP2 uses seeds computed by SpEED
- M. David, M. Dzamba, D. Lister, L. Ilie, and M. Brudno, SHRiMP2: Sensitive yet practical short read mapping, Bioinformatics 27(7) (2011) 1011 -- 1012.