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A genome assembler designed specifically for diploid highly polymorphic genomes based on SPAdes. dipSPAdes takes advantage of divergence between haplomes in repetitive genome regions to resolve them and construct longer contigs. It produces consensus contigs (representing a consensus of both haplomes for the orthologous regions) and performs haplotype assembly. Note that dipSPAdes can only benefit from high polymorphism rate (at least 0.4%). For the data with low polymorphism rate no improvement in terms of N50 vs conventional assemblers is expected.

Software type:
Command line interface
Restrictions to use:
Input data:
Reads, Haplocontigs
Operating system:
Unix/Linux, Mac OS
Programming languages:
GNU General Public License version 2.0
Computer skills:
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  • dipSPAdes <spades.support at bioinf.spbau.ru>

Additional informations

dipSPAdes comes as a part of SPAdes assembler package.

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