BWA

swMATH34374MaRDI QIDQ46083FDOQ46083

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Official website: http://bio-bwa.sourceforge.net

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

Cited In (only showing first 100 items - show all)

• 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
• When a dollar makes a BWT
• Computing the multi-string BWT and LCP array in external memory
• MONI
• 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
• Instance guaranteed ratio on greedy heuristic for genome scaffolding
• Wheeler graphs: a framework for BWT-based data structures
• 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
• BrownieAligner
• HMD-ARG
• A Bayesian nonparametric model for inferring subclonal populations from structured DNA sequencing data
• A randomized numerical aligner (rNA)
• Analytic combinatorics for computing seeding probabilities
• DNA-seq error correction based on substring indices
• Mason
• Indeterminate string factorizations and degenerate text transformations
• r-indexing the eBWT
• Refining the \(r\)-index
• Designing efficient spaced seeds for SOLiD read mapping
• 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
• Space efficient merging of de Bruijn graphs and Wheeler graphs
• Average-case linear-time similar substring searching by the \(q\)-gram distance
• AStarix
• Binning_refiner
• CLMB
• DLBI
• fastp
• GTDB-Tk
• metaGEM
• MetaWRAP
• Asgan
• hybridSPAdes
• Vargas
• 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
• GraphAligner
• ART
• Compressed directed acyclic word graph with application in local alignment
• Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem
• \textsc{AStarix}: fast and optimal sequence-to-graph alignment
• On the string matching with \(k\) mismatches
• CLMB: deep contrastive learning for robust metagenomic binning
• Full-text indexes for high-throughput sequencing
• Comparative assessment of alignment algorithms for NGS data: features, considerations, implementations, and future
• String-matching and alignment algorithms for finding motifs in NGS data
• SPUMONI
• TwoPaCo
• De Novo NGS Data Compression
• SpliceTAPyR -- an efficient method for transcriptome alignment
• TreeClone: reconstruction of tumor subclone phylogeny based on mutation pairs using next generation sequencing data
• Approximate string matching using a bidirectional index
• Soap
• casper
• BM-map
• GapsMis
• CloudBurst
• GATK
• Quake
• SOAP3
• GRASS
• SOPRA
• HiTEC
• countmotif
• miRBase
• fsaLib
• Samtools
• VCFtools
• SnpEff
• Artemis
• SHRiMP
• Meta-IDBA
• Velvet
• Cogent
• SeqAn
• BFAST
• PatternHunter
• ALFRED
• CLUSS
• FlyBase
• RazerS
• HIVE-hexagon
• BEETL

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