Disentangled long-read de Bruijn graphs via optical maps

DOI10.4230/LIPICS.WABI.2017.1MaRDI QIDQ5111789zbMATHOpenAlexFDO

Authors Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, 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

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)

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

Cites work

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

Cited in

(2)

• Fast and efficient Rmap assembly using the bi-labelled de Bruijn graph
• Kermit: guided long read assembly using coloured overlap graphs

Describes a project that uses

Uses Software

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

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