BWA

swMATH34374MaRDI QIDQ46083

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

Related Items (51)

Algorithmic Framework for Approximate Matching Under Bounded Edits with Applications to Sequence Analysis ⋮ Indeterminate string factorizations and degenerate text transformations ⋮ AStarix: Fast and Optimal Sequence-to-Graph Alignment ⋮ Approximate string matching using a bidirectional index ⋮ Approximate search of short patterns with high error rates using the \(01^\ast 0\) lossless seeds ⋮ Analytic combinatorics for computing seeding probabilities ⋮ r-indexing the eBWT ⋮ Fast and optimal sequence-to-graph alignment guided by seeds ⋮ CLMB: deep contrastive learning for robust metagenomic binning ⋮ On statistical modeling of sequencing noise in high depth data to assess tumor evolution ⋮ Compressed directed acyclic word graph with application in local alignment ⋮ Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem ⋮ Wheeler graphs: a framework for BWT-based data structures ⋮ Multi-pattern matching with bidirectional indexes ⋮ Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding ⋮ An algorithm for mapping short reads to a dynamically changing genomic sequence ⋮ Approximate all-pairs suffix/prefix overlaps ⋮ Unnamed Item ⋮ A survey of string orderings and their application to the Burrows-Wheeler transform ⋮ FM-index of alignment with gaps ⋮ A novel specialized single-linkage clustering algorithm for taxonomically ordered data ⋮ Extending alignments with \(k\)-mismatches and \(\ell\)-gaps ⋮ Average-case linear-time similar substring searching by the \(q\)-gram distance ⋮ Computing the Burrows-Wheeler transform of a string and its reverse in parallel ⋮ When a dollar makes a BWT ⋮ SpliceTAPyR — An Efficient Method for Transcriptome Alignment ⋮ Quantifying alternative splicing from paired-end RNA-sequencing data ⋮ Designing Efficient Spaced Seeds for SOLiD Read Mapping ⋮ Applying the positional Burrows-Wheeler transform to all-pairs Hamming distance ⋮ Full-Text Indexes for High-Throughput Sequencing ⋮ De Novo NGS Data Compression ⋮ DNA-Seq Error Correction Based on Substring Indices ⋮ Comparative Assessment of Alignment Algorithms for NGS Data: Features, Considerations, Implementations, and Future ⋮ CUSHAW Suite: Parallel and Efficient Algorithms for NGS Read Alignment ⋮ String-Matching and Alignment Algorithms for Finding Motifs in NGS Data ⋮ On the string matching with \(k\) mismatches ⋮ A space-efficient alphabet-independent Four-Russians' lookup table and a multithreaded Four-Russians' edit distance algorithm ⋮ Variance in estimated pairwise genetic distance under high versus low coverage sequencing: the contribution of linkage disequilibrium ⋮ A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data ⋮ Computing the multi-string BWT and LCP array in external memory ⋮ A randomized numerical aligner (rNA) ⋮ A resource-frugal probabilistic dictionary and applications in bioinformatics ⋮ Exome sequencing identifies predisposing and fusion gene in ganglioneuroma, ganglioneuroblastoma and neuroblastoma ⋮ Refining the \(r\)-index ⋮ The alternating BWT: an algorithmic perspective ⋮ A Bayesian feature allocation model for tumor heterogeneity ⋮ Wheeler languages ⋮ TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data ⋮ Global and local sequence alignment with a bounded number of gaps ⋮ Computing the Burrows-Wheeler transform in place and in small space ⋮ Space efficient merging of de Bruijn graphs and Wheeler graphs

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