Metassembler

Metassembler merges outputs from multiple de novo short-read assemblers, including SOAPdenovo and ALLPATHS-LG, to produce an improved consensus genome assembly with increased contiguity and sequence quality.

Key Features:

• Assembly Reconciliation (Metassembly): Merges multiple genome assemblies into a single consensus sequence by leveraging complementary strengths of constituent de novo short-read assemblies.
• Improved Contiguity and Quality: Demonstrates enhancements in contiguity and sequence quality on Assemblathon competition datasets.
• Systematic Evaluation and Guidelines: Includes a systematic evaluation of 120 permutations of the top five assemblies from the first Assemblathon competition and provides guidelines for effective meta-assembly.

Scientific Applications:

• Genome assembly projects: Reconciles outputs of multiple de novo short-read assemblers (e.g., SOAPdenovo, ALLPATHS-LG) to produce a more accurate and contiguous genome assembly.
• Gene annotation: Produces higher-contiguity assemblies that support more reliable gene annotation.
• Comparative genomics: Provides improved reference assemblies for comparative analyses across genomes.
• Evolutionary studies: Enables evolutionary analyses that require accurate and contiguous genome sequences.

Methodology:

Metassembler applies a strategic merging process that capitalizes on complementary attributes of input assemblies by systematically evaluating permutations of assembly combinations to identify configurations that maximize contiguity and sequence quality.