Hamid Mohamadi

ntHits: de novo repeat identification of genomics data using a streaming approach

ntHits identifies repeat elements in genomics data using a streaming algorithm, efficiently detecting repetitive k-mers with high accuracy and low resource usage.

RNA-Bloom provides lightweight reference-free transcriptome assembly for single cells

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

ntEdit: scalable genome sequence polishing

ntEdit is a genome polishing tool that efficiently corrects base errors in genomic sequences across various species and coverage levels.

Tigmint: Correcting Assembly Errors Using Linked Reads From Large Molecules

Tigmint corrects genome assembly errors using linked reads from long molecules, improving assembly contiguity and reducing misassemblies.

Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters

The paper introduces a multi-index Bloom filter for alignment-free sequence classification, showing improved sensitivity and efficiency over existing methods in read binning and taxonomic assignment.

Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms

The paper reviews and benchmarks overlap detection tools for error-prone long reads, evaluating their performance, efficiency, and scalability.

ABySS 2.0: Resource-Efficient Assembly of Large Genomes using a Bloom Filter

ABySS 2.0 improves genome assembly efficiency using Bloom filters, achieving high contiguity with reduced memory usage.