Comparative Assessment of Alignment Algorithms for NGS Data: Features, Considerations, Implementations, and Future

DOI10.1007/978-3-319-59826-0_9zbMath1457.68339MaRDI QIDQ3305532

Jimmy Lin, Carol Shen, Tony Shen

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_9

Mathematics Subject Classification ID

92D20: Protein sequences, DNA sequences

92D10: Genetics and epigenetics

68W32: Algorithms on strings

Uses Software

• STAR
• Soap
• SHRiMP
• PatternHunter
• HIVE-hexagon
• BS Seeker
• Bismark
• BSMAP
• Bowtie 2
• MapSplice
• CUSHAW
• Socrates
• MAP-RSeq
• Pash
• CAP-miRSeq
• PSAR-Align
• BatMeth
• BWA

Cites Work

• Alignment of trees -- an alternative to tree edit
• Simple Fast Algorithms for the Editing Distance between Trees and Related Problems