REAPR: a universal tool for genome assembly evaluation

The C.A.Ve. Software Tool for Genome Assembly

Misassembly due to the presence of repetitive DNA sequences often complicates the contig assembly stage of genome sequencing. Accurate physical representations of chromosomes, such as restriction maps or contig maps, provide a means for validating the sequence assembly and clarifying alignment ambiguity. The Contig Assembly Verifier (CAVe) software tool allows the researcher to automatically re...

GATB: Genome Assembly & Analysis Tool Box

MOTIVATION Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. RESULTS We propose an open-source library dedicated to genome assembly and analysis to fasten the pr...

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GAGE: A critical evaluation of genome assemblies and assembly

New sequencing technology has dramatically altered the landscape of whole-­‐genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-­‐cost technology can generate deep coverage of most species, including mammals...

GAGE: A critical evaluation of genome assemblies and assembly algorithms.

New sequencing technology has dramatically altered the landscape of whole-genome sequencing, allowing scientists to initiate numerous projects to decode the genomes of previously unsequenced organisms. The lowest-cost technology can generate deep coverage of most species, including mammals, in just a few days. The sequence data generated by one of these projects consist of millions or billions ...