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Integrating long-range connectivity information into de Bruijn graphs [article]

Isaac Turner, Kiran V. Garimella, Zamin Iqbal, Gil McVean
2017 bioRxiv   pre-print
Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph.  ...  However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data.  ...  Acknowledgements We thank Jerome Kelleher for his many useful comments and edits, Rachel Norris for her pointers and insight into the K. pneumoniae dataset, and the other members of the McVean group for  ... 
doi:10.1101/147777 fatcat:pd5gmzelkfbu5oiqdd4upkftve

Integrating long-range connectivity information into de Bruijn graphs

Isaac Turner, Kiran V Garimella, Zamin Iqbal, Gil McVean, Bonnie Berger
2018 Bioinformatics  
Constructed by adding annotations on top of a de Bruijn graph, it stores long range connectivity information through the graph.  ...  However, unlike the string graph, a de Bruijn graph does not retain long range information that is inherent in the read data.  ...  Acknowledgements We thank Jerome Kelleher for his many useful comments and edits, Rachel Norris for her pointers and insight into the K. pneumoniae dataset, and the other members of the McVean group for  ... 
doi:10.1093/bioinformatics/bty157 pmid:29554215 pmcid:PMC6061703 fatcat:7ksbpf6i7nfofajzazgezy5ohe

An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search [article]

Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson, Rob Patro
2018 bioRxiv   pre-print
the de Bruijn graph (dbg).  ...  The colored de Bruijn graph (cdbg) and its variants have become an important combinatorial structure used in numerous areas in genomics, such as population-level variation detection in metagenomic samples  ...  that needs to store color information over a large de Bruijn graph.  ... 
doi:10.1101/464222 fatcat:v67zaohurfcqnou4deeurv5oxa

The Theory and Practice of Genome Sequence Assembly

Jared T. Simpson, Mihai Pop
2015 Annual review of genomics and human genetics (Print)  
The paired de Bruijn graph (64) and pathset graph (87) approaches modify the de Bruijn graph structure to implicitly encode the mate-pair information, thereby resolving segments of the graph that are consistent  ...  Second, transitive edges are removed from the graph. The resulting graph, called a string graph, shares many properties with the de Bruijn graph without the need to break the reads into k-mers.  ... 
doi:10.1146/annurev-genom-090314-050032 pmid:25939056 fatcat:iayzwkwyljey5nn6hyxhwgsg7u

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis [article]

Yuzhen Ye, Haixu Tang
2015 arXiv   pre-print
Here we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies.  ...  A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph.  ...  sequences connecting long contigs.  ... 
arXiv:1504.01304v1 fatcat:qn52jf57pvfvtdgptvnpjtja24

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

E. Bao, T. Jiang, T. Girke
2014 Bioinformatics  
From the obtained alignments, it builds a novel data structure, called the PE multipositional de Bruijn graph.  ...  Motivation: De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs.  ...  ACKNOWLEDGEMENT The authors acknowledge the support of the core facilities at the Institute for Integrative Genome Biology (IIGB) at University of California (UC), Riverside.  ... 
doi:10.1093/bioinformatics/btu291 pmid:24932000 pmcid:PMC4058956 fatcat:px75xla3zrh6lcnyea45olnvi4

A Computer Simulator for Assessing Different Challenges and Strategies of de Novo Sequence Assembly

Bjarne Knudsen, Roald Forsberg, Michael M. Miyamoto
2010 Genes  
We illustrate the application and utility of our new simulation tools with several experiments that test the effects of genome complexity (repeats), read length and coverage, word size in De Bruijn graph  ...  This study presents a new computer program for assessing the effects of different factors and sequencing strategies on de novo sequence assembly.  ...  In effect, the first 15 nucleotides of this read are discarded by the De Bruijn graph algorithm, thereby making it more difficult to connect reads into contigs by their minimal overlaps [2] .  ... 
doi:10.3390/genes1020263 pmid:24710045 pmcid:PMC3954094 fatcat:vrhkjv76wzgqtox6cjygvnvave

HINGE: long-read assembly achieves optimal repeat resolution

Govinda M. Kamath, Ilan Shomorony, Fei Xia, Thomas A. Courtade, David N. Tse
2017 Genome Research  
As a result, HINGE combines the error resilience of overlap-based assemblers with repeat-resolution capabilities of de Bruijn graph assemblers.  ...  Long-read sequencing technologies have the potential to produce gold-standard de novo genome assemblies, but fully exploiting error-prone reads to resolve repeats remains a challenge.  ...  to what is achieved with de Bruijn graphs.  ... 
doi:10.1101/gr.216465.116 pmid:28320918 pmcid:PMC5411769 fatcat:4x2myklanjbnhn5436vki4fzk4

Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis

Yuzhen Ye, Haixu Tang
2015 Bioinformatics  
Results: Here, we report a reads mapping algorithm for mapping of short reads onto a de Bruijn graph of assemblies.  ...  A hash table of junction k-mers (k-mers spanning branching structures in the de Bruijn graph) is used to facilitate fast mapping of reads to the graph.  ...  sequences connecting long contigs.  ... 
doi:10.1093/bioinformatics/btv510 pmid:26319390 pmcid:PMC4896364 fatcat:xy3ecv4wa5aflajoehhw4gy23y

IDBA-tran: a more robust de novo de Bruijn graph assembler for transcriptomes with uneven expression levels

Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Ming-Ju Lv, Xin-Guang Zhu, Francis Y. L. Chin
2013 Bioinformatics  
One challenge is to remove erroneous vertices/ edges with high multiplicity (produced by high-expressed isoforms) in the de Bruijn graph without removing correct ones with not-sohigh multiplicity from  ...  Like de novo genome assembly, de novo transcriptome assembly does not rely on any reference genome or additional annotation information, but is more difficult.  ...  The depth information is used to separate de Bruijn graph into components. Ideally, transcripts from different genes are decomposed into different components.  ... 
doi:10.1093/bioinformatics/btt219 pmid:23813001 pmcid:PMC3694675 fatcat:rh7af7gvozed3p4mdeytmojuba

Assembling Long Accurate Reads Using de Bruijn Graphs [article]

Anton Bankevich, Andrey V Bzikadze, Mikhail Kolmogorov, Pavel Pevzner
2020 bioRxiv   pre-print
Since the de Bruijn graph constructed for a fixed k-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varying k-mer sizes.  ...  Although the de Bruijn graphs represent the basis of many genome assemblers, it remains unclear how to construct these graphs for large genomes and large k-mer sizes.  ...  The iterative de Bruijn graph approach (Peng et al., 2010) addresses this challenge by incorporating information about the de Bruijn graphs for a range of parameters k 1 < k 2 < … < k t into the de Bruijn  ... 
doi:10.1101/2020.12.10.420448 fatcat:euaezkb5czfmpfhdjfj2vsjgiq

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney
2012 Bioinformatics  
In the absence of a known genome, it is necessary to assemble these sequences de novo, taking into account possible alternative isoforms and the dynamic range of expression values.  ...  It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.  ...  Trinity starts by extending contigs greedily, connecting them into a de Bruijn graph, then extracting sufficiently covered paths through this graph.  ... 
doi:10.1093/bioinformatics/bts094 pmid:22368243 pmcid:PMC3324515 fatcat:mxbrrybygzgpdar5jtht5ibnmm

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

Toshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara
2012 Nucleic Acids Research  
Our fundamental concept was to first decompose a de Bruijn graph constructed from mixed short reads into individual sub-graphs, and second, to build scaffolds based on each decomposed de Bruijn sub-graph  ...  We made use of two features, the coverage (abundance) difference and graph connectivity, for the decomposition of the de Bruijn graph.  ...  (Decomposition by connectivity) Decompose the initial de Bruijn graph into connected subgraphs. 6.  ... 
doi:10.1093/nar/gks678 pmid:22821567 pmcid:PMC3488206 fatcat:6qrq37aex5hvdnf6ifcmazqps4

De novo repeat classification and fragment assembly

Pavel A. Pevzner, Haixu Tang, Glenn Tesler
2004 Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04  
For a vertex v, let P(v) be the set of positions in the connected component of the A-graph that was merged into v in the process of the A-Bruijn graph construction.  ...  Bulges and whirls may further aggregate into networks of bulges/ whirls that complicate the analysis of the A-Bruijn graph (as compared with the de Bruijn graph) and hide the underlying repeat structure  ... 
doi:10.1145/974614.974643 dblp:conf/recomb/PevznerTT04 fatcat:wfgtq6ypinf6npzynot7lzc464

A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data

Despoina D. Roumpeka, R. John Wallace, Frank Escalettes, Ian Fotheringham, Mick Watson
2017 Frontiers in Genetics  
De novo assembly software tools use one of two main paradigms: OLC or the de Bruijn graph approach. Both algorithms are based on graphs consisted of nodes connected with edges.  ...  Many more recent de novo assemblers use the de Bruijn graph approach (Pevzner et al., 2001) which constructs a graph by reading the consecutive kmers (sequences of k bases long) within each read.  ... 
doi:10.3389/fgene.2017.00023 pmid:28321234 pmcid:PMC5337752 fatcat:gp3iw2qoeve7bgwam7eqbln36e
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