Minimus: a fast, lightweight genome assembler
Sommer, Daniel D.
Delcher, Arthur L.
Salzberg, Steven L.
Minimus: a fast, lightweight genome assembler. D.D. Sommer, A.L. Delcher, S.L. Salzberg, and M. Pop. BMC Bioinformatics 2007 Feb 26;8:64.
MetadataShow full item record
Background: Genome assemblers have grown very large and complex in response to the need for algorithms to handle the challenges of large whole-genome sequencing projects. Many of the most common uses of assemblers, however, are best served by a simpler type of assembler that requires fewer software components, uses less memory, and is far easier to install and run. Results: We have developed the Minimus assembler to address these issues, and tested it on a range of assembly problems. We show that Minimus performs well on several small assembly tasks, including the assembly of viral genomes, individual genes, and BAC clones. In addition, we evaluate Minimus' performance in assembling bacterial genomes in order to assess its suitability as a component of a larger assembly pipeline. We show that, unlike other software currently used for these tasks, Minimus produces significantly fewer assembly errors, at the cost of generating a more fragmented assembly. Conclusion: We find that for small genomes and other small assembly tasks, Minimus is faster and far more flexible than existing tools. Due to its small size and modular design Minimus is perfectly suited to be a component of complex assembly pipelines. Minimus is released as an open-source software project and the code is available as part of the AMOS project at Sourceforge.
Showing items related by title, author, creator and subject.
Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath) Ward, Naomi; Larsen, Øivind; Sakwa, James; Bruseth, Live; Khouri, Hoda; Durkin, A. Scott; Dimitrov, George; Jiang, Lingxia; Scanlan, David; Kang, Katherine H.; Lewis, Matt; Nelson, Karen E.; Methe´, Barbara; Wu, Martin; Heidelberg, John F.; Paulsen, Ian T.; Fouts, Derrick; Ravel, Jacques; Tettelin, Herve; Ren, Qinghu; Read, Tim; DeBoy, Robert T.; Seshadri, Rekha; Salzberg, Steven L.; Jensen, Harold B.; Birkeland, Nils Kare; Nelson, William C.; Dodson, Robert J.; Grindhaug, Svenn H.; Holt, Ingeborg; Eidhammer, Ingvar; Jonasen, Inge; Vanaken, Susan; Utterback, Terry; Feldblyum, Tamara V.; Fraser, Claire M.; Lillehaug, Johan R.; Eisen, Jonathan A. (PLoS Biology, 2004-10)Methanotrophs are ubiquitous bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing ...
Angiuoli, Samuel V; Dunning Hotopp, Julie C; Salzberg, Steven L; Tettelin, Herve (2011-06-30)Background: Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes) is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors ...
Nagarajan, Niranjan; Cook, Christopher; Di Bonaventura, MariaPia; Ge, Hong; Richards, Allen; Bishop-Lilly, Kimberly A; DeSalle, Robert; Read, Timothy D; Pop, Mihai (2010-04-16)While new sequencing technologies have ushered in an era where microbial genomes can be easily sequenced, the goal of routinely producing high-quality draft and finished genomes in a cost-effective fashion has still ...