String graph based genome assembly software and tools !
...rbin. iii) Simpson-Durbin algorithm is that it does not rely on de Bruijn graphs, and instead employs a...or de novo genome assembly. As opposed to most assemblers, which are de Bruijn graph based, SAGE uses the st...2343 days ago
Bioinformatics tools developed for Oxford Nanopore data analysis !
...types of algorithms, such as greedy, overlap-layout-consensus (OLC), de Bruijn graph (DBG), and string graph...tegrateOLChttps://github.com/mariokostelac/ra-integrate/ ALLPATHS-LGde Bruijn graph ALLPATHS-L correctorhtt...2335 days ago
Bioinformatics algorithms tutorials
Useful bioinformatics tutorial, such as De Bruijn Graphs for NGS AssemblyAlgorithms for PacBio ReadsSoftware and Hardware Concepts for BioinformaticsFinding us in Homolog.us (Search...3618 days ago
RNA-Seq De novo Assembly Using Trinity
...seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the...clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Each...2980 days ago
Genome Assembly Tools and Software - PART2 !!
...ASHA is a parallel short read assembler for large genomes using de Bruijn graphs. Taking advantage of b...ssively parallel sequencing platforms. IDBA / IDBA-UD 1.1.1 – De Bruijn Graph De Novo Assembler with...2700 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...edvedev et al., Bioinformatics 27(13):i137-41, 2011. PubMedCentral De novo assembly Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Zerbino & Birney,...3794 days ago
Commercial and public next-gen-seq (NGS) software
...l. Linux/Win. EULER-SR - Short read de novo assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach. MIRA2 - MIRA...3533 days ago
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wtdbg2: A fuzzy Bruijn graph approach to long noisy reads assembly
Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output. ./wtdbg2 -x rs -g 4.6m -t 16 -i reads.fa.gz -fo p...Tags: wtdbg2, fuzzy, Bruijn, graph, approach, long, noisy, reads, assembly
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Comment on "Sibelia: A comparative genomics tool"
...Sequences file 2. Dot file with resulting de Bruijn graph All these files are...n slows down the computation. Resulting de Bruijn graph ----------------------...t value of K --------------- In "Sibelia" de Bruijn graph is constructed (N + 1)...1299 days ago
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