IDBA - A Practical Iterative de Bruijn Graph De Novo Assembler
By Yu Peng, Henry C. M. Leung, Siu Ming Yiu, Francis Y. L. Chin. Annual International Conference on Research in Computational Molecular Biology, 2010
300 citations recorded by the source corpus.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/491a17f486e085ad341b90cf8536b8ce57ef1f97
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In Artificial Intelligence
- Heng Li
- Steven L. Salzberg
- Jared T. Simpson
- Richard Durbin
- Fritz J. Sedlazeck
- Florian P. Breitwieser
- Michael C. Schatz
- Sergey Koren
In Molecular Biology
- Steven L. Salzberg
- Heng Li
- Adam M. Phillippy
- Sergey Koren
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- Florian P. Breitwieser
- Pavel A. Pevzner
- Jennifer Lu
Citations in the corpus
- Specialized metabolic functions of keystone taxa sustain soil microbiome stability (2021, methodology): “1 [38], and then filtered using a minimum length of 150 bp.”
- A review of methods and databases for metagenomic classification and assembly (2019, methodology): “The IDBA assembler (Iterative De Bruijn Graph Assembler) [125] first implemented this approach going from small k’s to large k’s, replacing reads”
- Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center (2016, methodology): “PATRIC provides several assembly strategies (Figure 3) that include algorithms for base calling correction [BayesHammer (12) and Kmer-genie (13)], and assemblers [Velvet (14), IDBA (15), Spades (16), MEGAHIT (17) and MiniASM (18)].”
- The khmer software package: enabling efficient nucleotide sequence analysis (2015, methodology): “The output of normalize-by-median.py can be assembled using a de novo assembler such as Velvet 10 , IDBA 11 , Trinity 12 or SPAdes 13 .”
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing (2012, methodology): “A similar approach was first introduced in the IDBA assembler (Peng et al., 2010).”
- The complete sequence of a human genome (2021, methodology): “This strategy is similar in spirit to the progressive increase of the k-mer size, commonly used by de Bruijn graph based assemblers (75).”
- An Integrated Pipeline for de Novo Assembly of Microbial Genomes (2012, methodology): “Using the newly cleaned reads derived from stage 1, stage 2 of the A5 pipeline builds contigs with the the assembler IDBA [28].”