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Genome profiling software tools | De novo genome sequencing data analysis

High throughput sequencing enables the sequencing of novel genomes on a daily basis. Nevertheless, even their most basic characteristics, such as their size or heterozygosity rate, may be initially unknown, making it difficult to select appropriate…
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SGA
Desktop

SGA String Graph Assembler

Assembles large genomes from high coverage short read data. SGA is designed as…

Assembles large genomes from high coverage short read data. SGA is designed as a modular set of programs, which are used to form an assembly pipeline. SGA implements a set of assembly algorithms…

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GenomeScope
Web
Desktop

GenomeScope

Estimates the overall genome characteristics (total and haploid genome length,…

Estimates the overall genome characteristics (total and haploid genome length, percentage of repetitive content, and heterozygosity rate) as well as overall read characteristics (read coverage, read…

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nQuire
Desktop

nQuire

Aims to distinguish the distribution of base frequencies at variable sites for…

Aims to distinguish the distribution of base frequencies at variable sites for diploids, triploids and tetraploids directly from read mappings to a reference genome. nQuire is a statistical approach…

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conPADE
Desktop

conPADE Contig Ploidy and Allele Dosage Estimation

A probabilistic method that estimates the ploidy of any given contig/scaffold…

A probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. ConPADE performs well as long as enough sequencing coverage is available, or the true…

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