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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…
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Slicembler
Desktop

Slicembler

A meta-assembler designed for ultra-deep sequencing data. Slicembler takes…

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…

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Metassembler
Desktop

Metassembler

Merges multiple assemblies of a genome into a single superior sequence. We…

Merges multiple assemblies of a genome into a single superior sequence. We apply it to the four genomes from the Assemblathon competitions and show it consistently and substantially improves the…

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GARM
Desktop

GARM Genome Assembler, Reconcilation and Merging

A software pipeline to merge and reconcile assemblies from different algorithms…

A software pipeline to merge and reconcile assemblies from different algorithms or sequencing technologies.

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CAMSA
Desktop

CAMSA Comparative Analysis and Merging of Scaffold Assemblies

A software tool for comparative analysis and merging of two or more given…

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…

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Zorro
Desktop

Zorro

A hybrid sequencing technology assembler. Zorro merges two sets of…

A hybrid sequencing technology assembler. Zorro merges two sets of pre-assembled contigs into a more contiguous and consistent assembly. The main feature of Zorro is the treatment before and after…

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GAA
Desktop

GAA Graph Accordance Assembly

Constructs an accordance graph to capture the mapping information between the…

Constructs an accordance graph to capture the mapping information between the target and query assemblies. Based on the accordance graph, the contigs or scaffolds of the target assembly can be…

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MAIA
Desktop

MAIA Multiple Assembly IntegrAtor

An assembly integrator that makes use of all available data, i.e. multiple de…

An assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria. The MAIA…

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CISA
Desktop

CISA Contig Integrator for Sequence Assembly

Integrates the assemblies into a hybrid set of contigs, resulting in assemblies…

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…

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Mix
Desktop

Mix

Mixes two or more draft assemblies, without relying on a reference genome and…

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…

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GAM-NGS
Desktop

GAM-NGS Genomic Assemblies Merger for Next Generation Sequencing

Merges two or more assemblies in order to enhance contiguity and correctness of…

Merges two or more assemblies in order to enhance contiguity and correctness of both. GAM-NGS does not rely on global alignment: regions of the two assemblies representing the same genomic locus…

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Minimus2
Desktop

Minimus2

Assemblies one or two sequence sets thanks to a nucmer based on overlap…

Assemblies one or two sequence sets thanks to a nucmer based on overlap detector. Minimus is a modified version of the minimus pipeline and is a part of the AMOS package.

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Tigmint
Desktop

Tigmint

Allows correction of misassemblies. Tigmint uses linked reads from 10x Genomics…

Allows correction of misassemblies. Tigmint uses linked reads from 10x Genomics Chromium for identifying misassemblies and improving the quality and contiguity of a de novo genome assembly.

PASA
Desktop

PASA Program to Assemble Spliced Alignments

Allows automation improvement of gene structures in Arabidopsis thaliana. PASA…

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…

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merger
Desktop

merger

Merges two overlapping sequences. merger reads two overlapping input sequences…

Merges two overlapping sequences. merger reads two overlapping input sequences of the same type (typically nucleotide). It uses a global alignment algorithm to optimally align the sequences and then…

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e-RGA
Desktop

e-RGA enhanced Reference Guided Assembly

Aims at producing an improve assembly in presence of a sequence belonging to a…

Aims at producing an improve assembly in presence of a sequence belonging to a closely related organism. The idea is to combine de novo and reference-guided assembly in order to obtain enhanced…

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