SpliceTAPyR -- an efficient method for transcriptome alignment

DOI10.1142/S0129054118430049MaRDI QIDQ5384621zbMATH OpenOpenAlexWikidataFDO

Authors Francisco E. jun. Fernandes, Alexandre P. Francisco, Andreia Sofia Teixeira

Publication date 24 June 2019

Published in International Journal of Foundations of Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1142/s0129054118430049

zbMATH Keywords

next-generation sequencingRNA-Seqsequence alignmentsplice junctionstranscriptome

Mathematics Subject Classification ID

Algorithms on strings (68W32) Protein sequences, DNA sequences (92D20)

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Cites work

• Compressed representations of sequences and full-text indexes
• Suffix Arrays: A New Method for On-Line String Searches

Cited in

(3)

• Comparison of BWA-MEM and NovoAlign using human whole-genome next-generation sequencing reads
• Yanagi: transcript segment library construction for RNA-seq quantification
• A practical fpt algorithm for F<scp>low</scp> D<scp>ecomposition</scp> and transcript assembly

Describes a project that uses

Uses Software

• STAR
• TopHat
• MapSplice
• BWA

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