AMAS: Optimizing the Partition and Filtration of Adaptive Seeds to Speed up Read Mapping
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- Type
- article
- Published
- 2015-02-18
- Cited by
- 9
- References
- 36
- Access
- Open access
- OpenAlex
- https://openalex.org/W1897953244
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:6621381
Keywords
Computer science, Memory footprint, Partition (number theory), Footprint, Data mining
References
- Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding
- Mason – A Read Simulator for Second Generation Sequencing Data
- Accelerating read mapping with FastHASH
- Streaming fragment assignment for real-time analysis of sequencing experiments
- mrsFast: a cache-oblivious algorithm for short-read mapping
- CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding
- The GEM mapper: fast, accurate and versatile alignment by filtration
- Identification of common molecular subsequences.
- A survey of sequence alignment algorithms for next-generation sequencing
- Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM
- Fast and SNP-tolerant detection of complex variants and splicing in short reads
- SOAP2: an improved ultrafast tool for short read alignment
- A fast bit-vector algorithm for approximate string matching based on dynamic programming
- Improving read mapping using additional prefix grams
- Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome.
- Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes
- A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues
- Sequencing technologies — the next generation
- Hobbes: optimized gram-based methods for efficient read alignment
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
Cited by
- Engineering Algorithms for Personal Genome Pipelines
- Development of a scalable, precise, and high-coverage genomics mapping tool for NGS
- Novel computational techniques for mapping and classifying Next-Generation Sequencing data. (Nouvelles techniques informatiques pour la localisation et la classification de données de séquençage haut débit)
- GRIM-filter: fast seed filtering in read mapping using emerging memory technologies
- GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies
- Accelerating Maximal-Exact-Match Seeding with Enumerated Radix Trees
- Space-efficient computation of parallel approximate string matching
- GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies
- Context-Aware Seeds for Read Mapping
- Context-Aware Seeds for Read Mapping
- Novel computational techniques for mapping and classification of Next-Generation Sequencing data
- Context-aware seeds for read mapping
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