BOL: Results for "de Bruijn"

Results for "de Bruijn"

- Rahul Nayak@rahul
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...
2342 days ago
- biogeek@biogeek
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...
2334 days ago
+1 more Blogs

- John Parker@parker
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...
3616 days ago
- Surabhi Chaudhary@surabhi
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...
2978 days ago
+18 more Bookmarks

- Rahul Nayak@rahul
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,...
3792 days ago
- Surabhi Chaudhary@surabhi
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...
3532 days ago
+7 more Top-level pages

- Jit@jit.aber
De #Bruijn #Graph #assembly http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf
2879 days ago
- Jit@jit.aber
De Bruijn graph Tutorial http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_dbg.pdf #Assembly #Tutorial #DeBruijn
2384 days ago
+3 more Wire posts

- Shruti Paniwala@shruti
Scalpel
...ng. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; howev...
3559 days ago

- Jit@jit.aber
Running Trinity on RNA-seq !
...ed -------------------------------------------------------- -------------------- Chrysalis ------------------------- -- (Contig Clustering & de Bruijn Graph Construction) -- -----...
2140 days ago
- Jit@jit.aber
Install Bwise using conda !
...ion: done Verifying transaction: done Executing transaction: done (JitMetaENV) ➜ test_phase_assebly bwise *** This is BWISE - High order De Bruijn graph assembler *** The co...
1003 days ago

- BioStar@biostar
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)...
1298 days ago
- Jit@jit.aber
Comment on "SPAdes"
Common usage SPAdes: de Bruijn graph based assembler The last assembler we will run is SPAdes. SPAdes is different from the other assemblers in that it generates a final...
2357 days ago
+2 more Comments