I am a postdoctoral researcher in the LAGE team at Genoscope. My research work focuses on algorithms and data structures for large-scale processing of complex sequencing banks as metagenomes from the Tara projet. Previously I have developed methods and tools for constructing, streaming and filtering k-mers matrices from large sequencing collections.

Publications

1. T. Lemane, Indexing and analysis of large sequencing collections using k-mer matrices, PhD Thesis, 2022. [PDF]
2. T. Lemane, R. Chikhi, P. Peterlongo, kmdiff, large-scale and user-friendly differential k-mer analyses, Bioinformatics, 2022. [PDF]
3. Y. Dufresne, T. Lemane, P. Marijon, P. Peterlongo, A. Rahman, M. Kokot, P. Medvedev, S. Deorowicz, R. Chikhi, The K-mer File Format: a standardized and compact disk representation of sets of k-mers, Bioinformatics, 2022. [PDF]
4. T. Lemane, P. Medvedev, R. Chikhi, P. Peterlongo, kmtricks: Efficient and flexible construction of Bloom filters for large sequencing data collections, Bioinformatics Advances, 2022. [PDF]
5. G. Siekaniec, E. Roux, T. Lemane, E. Guédon, J. Nicolas, Identification of isolated or mixed strains from long reads: a challenge met on Streptococcus thermophilus using a MinION sequencer, Microbial Genomics, 2021. [PDF]

Software

• kmtricks: kmtricks is a tool suite for counting k-mers, and constructing bloom filters or counted kmer matrices from large and numerous read sets.
• kmdiff: kmdiff is a tool allowing differential k-mers analysis on large cohorts.
• kmindex: kmindex is a tool for querying presence/absence k-mer matrices computed by kmtricks.

Talks

• JOBIM 2022 kmtricks: creating bloom filters for indexing large sequencing data collection. [slides]
• SeqBIM 2021 Advances in k-mer matrix construction for analysis of large sequencing collections. [slides]
• SeqBIM 2020 kmtricks: modular k-mer count matrix and Bloom filter construction for large read collections [slides]
• DSB 2020 HowDeSBT and Simka wedding: what as been done and what we plan to do ? [slides]

Teaching

• 2019-2021: Strings algorithms and bioinformatics, MSc1 Software Engineering, ISTIC