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Bit-parallel sequence-to-graph alignment

https://doi.org/10.1101/323063
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/3-540-61258-0_1openalex-snapshot
A faster algorithm for approximate string matching
inferredcites →https://doi.org/10.1007/bf02458834openalex-snapshot
Approximate matching of regular expressions
inferredcites →https://doi.org/10.1016/0022-2836(70)90057-4openalex-snapshot
A general method applicable to the search for similarities in the amino acid sequence of two proteins
inferredcites →https://doi.org/10.1016/0022-2836(81)90087-5openalex-snapshot
Identification of common molecular subsequences
inferredcites →https://doi.org/10.1016/0196-6774(80)90016-4openalex-snapshot
The theory and computation of evolutionary distances: Pattern recognition
inferredcites →https://doi.org/10.1016/0196-6774(85)90023-9openalex-snapshot
Finding approximate patterns in strings
inferredcites →https://doi.org/10.1016/j.ygeno.2010.03.001openalex-snapshot
Assembly algorithms for next-generation sequencing data
inferredcites →https://doi.org/10.1016/s0304-3975(99)00333-3openalex-snapshot
Improved approximate pattern matching on hypertext
inferredcites →https://doi.org/10.1017/cbo9781139940023openalex-snapshot
Genome-Scale Algorithm Design
inferredcites →https://doi.org/10.1038/nbt.2023openalex-snapshot
How to apply de Bruijn graphs to genome assembly
inferredcites →https://doi.org/10.1038/nbt.4227openalex-snapshot
Variation graph toolkit improves read mapping by representing genetic variation in the reference
inferredcites →https://doi.org/10.1089/cmb.2017.0264openalex-snapshot
Sequence Alignment on Directed Graphs
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.452openalex-snapshot
Multiple sequence alignment using partial order graphs
inferredcites →https://doi.org/10.1093/bioinformatics/bts649openalex-snapshot
PBSIM: PacBio reads simulator—toward accurate genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btu538openalex-snapshot
LoRDEC: accurate and efficient long read error correction
inferredcites →https://doi.org/10.1093/bioinformatics/btv383openalex-snapshot
Bandage: interactive visualization of de novo genome assemblies
inferredcites →https://doi.org/10.1093/bioinformatics/btv688openalex-snapshot
hybrid SPA des : an algorithm for hybrid assembly of short and long reads
inferredcites →https://doi.org/10.1101/gr.214155.116openalex-snapshot
Genome graphs and the evolution of genome inference
inferredcites →https://doi.org/10.1145/135239.135243openalex-snapshot
A new approach to text searching
inferredcites →https://doi.org/10.1145/316542.316550openalex-snapshot
A fast bit-vector algorithm for approximate string matching based on dynamic programming
inferredcites →https://doi.org/10.1186/1471-2105-15-99openalex-snapshot
Genome alignment with graph data structures: a comparison
inferredcites →https://doi.org/10.1186/s12859-016-1103-9openalex-snapshot
Read mapping on de Bruijn graphs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-031-04749-7_22openalex-snapshot
Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa265openalex-snapshot
Vargas: heuristic-free alignment for assessing linear and graph read aligners
inferred← citeshttps://doi.org/10.1101/2020.01.22.915496openalex-snapshot
AStarix: Fast and Optimal Sequence-to-Graph Alignment
inferred← citeshttps://doi.org/10.1101/2020.01.27.921338openalex-snapshot
AERON: Transcript quantification and gene-fusion detection using long reads
inferred← citeshttps://doi.org/10.1101/673624openalex-snapshot
Read correction for non-uniform coverages
inferred← citeshttps://doi.org/10.1109/ipdps.2019.00055openalex-snapshot
Accelerating Sequence Alignment to Graphs
inferred← citeshttps://doi.org/10.1186/s12859-020-03590-7openalex-snapshot
SPAligner: alignment of long diverged molecular sequences to assembly graphs
inferred← citeshttps://doi.org/10.12688/f1000research.20233.1openalex-snapshot
A Sequence Distance Graph framework for genome assembly and analysis
inferred← citeshttps://doi.org/10.18174/589859openalex-snapshot
Unlocking the secrets of Brassica oleracea crops : A genomic journey
inferred← citeshttps://doi.org/10.5220/0011666900003414openalex-snapshot
Fast Exact String to D-Texts Alignments
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