Disentangled long-read de Bruijn graphs via optical maps

DOI10.4230/LIPICS.WABI.2017.1zbMATH Open1443.92132OpenAlexW3021341025MaRDI QIDQ5111789FDOQ5111789

Simon J. Puglisi, Leena Salmela, Bahar Alipanahi, Martin D. Muggli, Christina Boucher

Publication date: 27 May 2020

Full work available at URL: https://drops.dagstuhl.de/opus/volltexte/2017/7661/pdf/LIPIcs-WABI-2017-1.pdf

Recommendations

• Fast and efficient Rmap assembly using the bi-labelled de Bruijn graph
• Kermit: guided long read assembly using coloured overlap graphs
• OMGS: optical map-based genome scaffolding
• From indexing data structures to de Bruijn graphs
• Safe and complete contig assembly via omnitigs

zbMATH Keywords

optical mapsPacBiopositional de Bruijn graph

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• An Eulerian path approach to DNA fragment assembly
• Succinct de Bruijn Graphs

Cited In (2)

• Kermit: Guided Long Read Assembly using Coloured Overlap Graphs
• Fast and efficient Rmap assembly using the bi-labelled de Bruijn graph

Uses Software

• SEQuel
• SPAdes
• Velvet
• QUAST
• ABySS
• OMBlast
• PBSIM
• Maligner
• Canu

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