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Assembly reconciliation software tools | De novo genome sequencing data analysis

The goal of assembly reconciliation is to merge the assemblies produced by different tools while detecting possible mis-assemblies and isolating problematic regions.

Source text:
(Vicedomini et al., 2013) GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics.

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PASA / Program to Assemble Spliced Alignments
Allows automation improvement of gene structures in Arabidopsis thaliana. PASA was used in Eukaryotic genome annotation projects such as Rice, Aspergillus species, Plasmodium falciparum, Schistosoma mansoni, Aedes aegypti, mouse, human, among others. This tool is able to recognize and organize splicing variations supported by the transcript alignments. It can clean the transcripts, validate perfect alignments or procced to automatic genome annotation.
Slicembler
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A meta-assembler designed for ultra-deep sequencing data. Slicembler takes advantage of the whole dataset, and significantly improves the final quality of the assembly. Slicembler partitions the input data into optimal-sized “slices” and uses a standard assembly tool (e.g., Velvet, SPAdes, IDBA, Ray) to assemble each slice individually. Slicembler uses majority voting among the individual assemblies to identify long contigs that can be merged to the consensus assembly. It extracts high-quality contigs from the slice assemblies, and prevents contigs containing mis-joins and calling errors to be included in the final assembly.
quickmerge
Improves contiguity of genome assemblies based on long molecule sequences. quickmerge merges assemblies to produce a more contiguous assembly. This software uses information from assemblies built with Pacific Biosciences of Oxford Nanopore long reads or Illumina short reads to enhance contiguities of an assembly generated with only long reads alone. It splices and merges contiguities without introducing any new assembly errors. It does not include spurious sequences or large scale missassemblies.
CISA / Contig Integrator for Sequence Assembly
Integrates the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. A user supplies a set of contigs from at least three assemblers in FASTA format to CISA to obtain integrated contigs.
Mix
Mixes two or more draft assemblies, without relying on a reference genome and having the goal to reduce contig fragmentation and thus speed-up genome finishing. Mix builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a set of paths in the extension graph that maximizes the cumulative contig length.
CAMSA / Comparative Analysis and Merging of Scaffold Assemblies
A software tool for comparative analysis and merging of two or more given scaffold assemblies. CAMSA takes as an input two or more assemblies of the same set of scaffolds and generates a comprehensive comparative report for them. The report not only contains multiple numerical characteristics for the input assemblies, but also provides an interactive framework for their visual comparison and analysis. CAMSA also computes a merged assembly, combining the input assemblies into more comprehensive one, which resolves conflicts and determine orientation of unoriented scaffolds in the most confident way.
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