Fragment assembly with short reads
Bioinformatics
The fragment assembly string graph
Bioinformatics
Assembling millions of short DNA sequences using SSAKE
Bioinformatics
Extending assembly of short DNA sequences to handle error
Bioinformatics
T-IDBA: a de novo iterative de bruijn graph assembler for transcriptome
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
Parallel and memory-efficient reads indexing for genome assembly
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part II
PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching problem, due to erroneous reads and repeat regions A proper choice of k is crucial but for single k there is always a trade-off: a small k favors the situation of erroneous reads and non-uniform coverage, and a large k favors short repeat regions. We propose an iterative de Bruijn graph approach iterating from small to large k exploring the advantages of the in between values Our IDBA outperforms the existing algorithms by constructing longer contigs with similar accuracy and using less memory, both with real and simulated data The running time of the algorithm is comparable to existing algorithms. Availability: IDBA is available at http://www.cs.hku.hk/~alse/idba/