BWA

swMATH34374MaRDI QIDQ46083FDOQ46083

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Source code repository: https://github.com/lh3/bwa

Cited In (51)

• SpliceTAPyR — An Efficient Method for Transcriptome Alignment
• Global and local sequence alignment with a bounded number of gaps
• Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis
• Extending alignments with \(k\)-mismatches and \(\ell\)-gaps
• Multi-pattern matching with bidirectional indexes
• TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data
• When a dollar makes a BWT
• Computing the multi-string BWT and LCP array in external memory
• Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance
• An algorithm for mapping short reads to a dynamically changing genomic sequence
• Approximate all-pairs suffix/prefix overlaps
• Wheeler languages
• Variance in estimated pairwise genetic distance under high versus low coverage sequencing: the contribution of linkage disequilibrium
• Wheeler graphs: a framework for BWT-based data structures
• CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment
• Computing the Burrows-Wheeler transform in place and in small space
• Approximate search of short patterns with high error rates using the \(01^\ast 0\) lossless seeds
• Title not available (Why is that?)
• Computing the Burrows-Wheeler transform of a string and its reverse in parallel
• Approximate string matching using a bidirectional index
• De Novo NGS Data Compression
• Comparative Assessment of Alignment Algorithms for NGS Data: Features, Considerations, Implementations, and Future
• Full-Text Indexes for High-Throughput Sequencing
• String-Matching and Alignment Algorithms for Finding Motifs in NGS Data
• A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data
• A randomized numerical aligner (rNA)
• Analytic combinatorics for computing seeding probabilities
• Indeterminate string factorizations and degenerate text transformations
• r-indexing the eBWT
• AStarix: Fast and Optimal Sequence-to-Graph Alignment
• Refining the \(r\)-index
• Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding
• A Bayesian feature allocation model for tumor heterogeneity
• Exome sequencing identifies predisposing and fusion gene in ganglioneuroma, ganglioneuroblastoma and neuroblastoma
• On statistical modeling of sequencing noise in high depth data to assess tumor evolution
• Fast and optimal sequence-to-graph alignment guided by seeds
• DNA-Seq Error Correction Based on Substring Indices
• Space efficient merging of de Bruijn graphs and Wheeler graphs
• Average-case linear-time similar substring searching by the \(q\)-gram distance
• Designing Efficient Spaced Seeds for SOLiD Read Mapping
• A resource-frugal probabilistic dictionary and applications in bioinformatics
• The alternating BWT: an algorithmic perspective
• A survey of string orderings and their application to the Burrows-Wheeler transform
• FM-index of alignment with gaps
• A space-efficient alphabet-independent Four-Russians' lookup table and a multithreaded Four-Russians' edit distance algorithm
• Quantifying alternative splicing from paired-end RNA-sequencing data
• A novel specialized single-linkage clustering algorithm for taxonomically ordered data
• Compressed directed acyclic word graph with application in local alignment
• Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem
• On the string matching with \(k\) mismatches
• CLMB: deep contrastive learning for robust metagenomic binning

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