Fully Dynamic de Bruijn Graphs

We present a space- and time-efficient fully dynamic implementation of de Bruijn graphs, which can also support fixed-length jumbled pattern matching.

[1]  Kurt Mehlhorn,et al.  On the program size of perfect and universal hash functions , 1982, 23rd Annual Symposium on Foundations of Computer Science (sfcs 1982).

[2]  Gregory Kucherov,et al.  Using Cascading Bloom Filters to Improve the Memory Usage for de Brujin Graphs , 2013, WABI.

[3]  Moshe Lewenstein,et al.  On Hardness of Jumbled Indexing , 2014, ICALP.

[4]  Dan Gusfield,et al.  Algorithms in Bioinformatics , 2002, Lecture Notes in Computer Science.

[5]  Gad M. Landau,et al.  Binary Jumbled Pattern Matching on Trees and Tree-Like Structures , 2013, ESA.

[6]  Veli Mäkinen,et al.  Indexing Graphs for Path Queries with Applications in Genome Research , 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[7]  Rayan Chikhi,et al.  Space-efficient and exact de Bruijn graph representation based on a Bloom filter , 2012, Algorithms for Molecular Biology.

[8]  Wojciech Rytter,et al.  Efficient Indexes for Jumbled Pattern Matching with Constant-Sized Alphabet , 2013, ESA.

[9]  Sebastiano Vigna,et al.  Monotone minimal perfect hashing: searching a sorted table with O(1) accesses , 2009, SODA.

[10]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[11]  Kunihiko Sadakane,et al.  Succinct de Bruijn Graphs , 2012, WABI.

[12]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[13]  Leena Salmela,et al.  LoRDEC: accurate and efficient long read error correction , 2014, Bioinform..

[14]  Richard M. Karp,et al.  Efficient Randomized Pattern-Matching Algorithms , 1987, IBM J. Res. Dev..

[15]  Christina Boucher,et al.  Variable-Order de Bruijn Graphs , 2014, 2015 Data Compression Conference.

[16]  Zsuzsanna Lipták,et al.  Algorithms for Jumbled Pattern Matching in Strings , 2011, Int. J. Found. Comput. Sci..

[17]  Marco Previtali,et al.  Bidirectional Variable-Order de Bruijn Graphs , 2016, LATIN.