SUTTA
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Application data |
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| Biological application domain(s) | Sequence assembly (de novo assembly) |
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| Created at | New York University |
| Maintained? | Maybe |
| Licence | Commercial, Freeware |
| Contact: | narzisi@nyu.edu |
Summary: De novo assembly algorithm for assembling bacterial genomes from second generation sequencing data
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Contents
Description
The current version of the SUTTA assembler is prototyped around the AMOS (A Modular Open-Source assembler) assembly framework. AMOS supports a central data repository of various genomic objects (reads, inserts, maps, overlaps, contigs, scaffolds, etc.) to be easily collected and indexed. The AMOS framework also provides several algorithms to perform some of the standard steps in the assembly pipeline (e.g., Sequence trimming, Overlapping, Error Correction, Scaffolding, Validation). SUTTA's pipeline is composed of three modules: (1) overlapper, (2) contigger, and (3) multi-aligner. We developed our tools for the first two steps, instead we relied on the "make-consensus module available in AMOS for the computation of the final consensus sequence.
For this reason, in order to use SUTTA, it is first required to install the AMOS package
Features
- Technology Agnostic: supports different set of technologies with minimal changes to its architecture (currently long Sanger reads and short next-generation Illumina reads). It can potentially use different long range technologies (mate-pairs, optical maps, dilution sequencing). Currently it supports standard mate-pair information available both for short and long reads.
- Search strategy: each contig (continuous sequence of the genome) is assembled independently and dynamically without creating in advance the graph that describes the overlapping relations between all the reads;
- Score-based: score functions are used to evaluate the DNA sequences concurrently while being assembled. The functions combine different structural properties (e.g., transitivity, coverage, mated pairs, physical maps, etc).
Links
References
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