Full-text indexes for high-throughput sequencing

DOI10.1007/978-3-319-59826-0_2MaRDI QIDQ3305517zbMATH OpenOpenAlexFDO

Authors David Weese, Enrico Siragusa

Publication date 7 August 2020

Published in Algorithms for Next-Generation Sequencing Data (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1007/978-3-319-59826-0_2

Mathematics Subject Classification ID

Data structures (68P05) Algorithms on strings (68W32)

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Cites work

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• An extension of the Burrows-Wheeler transform
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• From indexing data structures to de Bruijn graphs
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• Lightweight algorithms for constructing and inverting the BWT of string collections
• Lightweight data indexing and compression in external memory
• On the sorting-complexity of suffix tree construction
• On-line construction of suffix trees
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• Suffix Arrays: A New Method for On-Line String Searches
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Cited in

(5)

• String-matching and alignment algorithms for finding motifs in NGS data
• Algorithms for indexing highly similar DNA sequences
• Algorithms for next-generation sequencing data. Techniques, approaches, and applications
• Indexing hypertext
• FEMTO: fast search of large sequence collections

Describes a project that uses

Uses Software

• BWA
• STELLAR
• MicroRazerS
• Fiona
• SeqAn
• PATRICIA
• Samtools

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