On the Complexity of Sequence-to-Graph Alignment

Availability of extensive genetic data across multiple individuals and populations is driving the growing importance of graph-based reference representations. Aligning sequences to graphs is a fund...

[1]  Tobias Marschall,et al.  Aligning sequences to general graphs in O(V + mE) time , 2017, bioRxiv.

[2]  P. Pevzner,et al.  An Eulerian path approach to DNA fragment assembly , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Ryan R. Wick,et al.  Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads , 2016, bioRxiv.

[4]  Gonzalo Navarro Improved approximate pattern matching on hypertext , 2000, Theor. Comput. Sci..

[5]  O. Gotoh An improved algorithm for matching biological sequences. , 1982, Journal of molecular biology.

[6]  Piotr Indyk,et al.  Edit Distance Cannot Be Computed in Strongly Subquadratic Time (unless SETH is false) , 2014, STOC.

[7]  Will P. M. Rowe,et al.  Indexed variation graphs for efficient and accurate resistome profiling , 2018, bioRxiv.

[8]  Gonzalo Navarro,et al.  A guided tour to approximate string matching , 2001, CSUR.

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

[10]  Chris Thachuk Indexing hypertext , 2013, J. Discrete Algorithms.

[11]  Gil McVean,et al.  Improved genome inference in the MHC using a population reference graph , 2014, Nature Genetics.

[12]  Dong Kyue Kim,et al.  String Matching in Hypertext , 1995, CPM.

[13]  Yves Van de Peer,et al.  BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs , 2018, BMC Bioinform..

[14]  Pierre Peterlongo,et al.  Read Mapping on de Bruijn graph , 2015, ArXiv.

[15]  Christopher J. Lee,et al.  Multiple sequence alignment using partial order graphs , 2002, Bioinform..

[16]  Srinivas Aluru,et al.  A comprehensive evaluation of long read error correction methods , 2019, BMC Genomics.

[17]  Moshe Lewenstein,et al.  Pattern Matching in Hypertext , 1997, J. Algorithms.

[18]  Paola Bonizzoni,et al.  Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext , 2017, AlCoB.

[19]  Shilpa Garg,et al.  A graph-based approach to diploid genome assembly , 2018, Bioinform..

[20]  Naveen Sivadasan,et al.  Sequence Alignment on Directed Graphs , 2017, bioRxiv.

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

[22]  Kari Stefansson,et al.  Graphtyper enables population-scale genotyping using pangenome graphs , 2017, Nature Genetics.

[23]  William Jones,et al.  Variation graph toolkit improves read mapping by representing genetic variation in the reference , 2018, Nature Biotechnology.

[24]  David Haussler,et al.  Building a Pan-Genome Reference for a Population , 2015, J. Comput. Biol..

[25]  Dmitry Antipov,et al.  hybridSPAdes: an algorithm for hybrid assembly of short and long reads , 2016, Bioinform..

[26]  Alexandru I. Tomescu,et al.  Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended , 2018, RECOMB.

[27]  Lin Huang,et al.  Short read alignment with populations of genomes , 2013, Bioinform..

[28]  Eugene W. Myers,et al.  The fragment assembly string graph , 2005, ECCB/JBI.

[29]  Ronald L. Rivest,et al.  Introduction to Algorithms, third edition , 2009 .

[30]  Pierre Peterlongo,et al.  Read mapping on de Bruijn graphs , 2015, BMC Bioinformatics.

[31]  Udi Manber,et al.  APPROXIMATE STRING MATCHING WITH ARBITRARY COSTS FOR TEXT AND HYPERTEXT , 1993 .

[32]  Yadong Wang,et al.  deBGA: read alignment with de Bruijn graph-based seed and extension , 2016, Bioinform..

[33]  Leonard McMillan,et al.  FMLRC: Hybrid long read error correction using an FM-index , 2018, BMC Bioinformatics.