The SPAdes assembler is developed by Algorithmic Biology Lab at the St. Petersburg Academic University.
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IDBA (iterative De Bruijn Graph De Novo Assembler) is developed by the Bioinfomatics Research Group in the department of Computer Science at the University of Hong Kong.
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The velvet optimiser tools tests multiple kmer values for velvet and returns the best assembly. This assembler is developed by the Victorian Bioinformatics Consortium.
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The velvet assembler was one of the first assemblers created for short read sequencing. Velvet was developed at the European Bioinformatics Institute.
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The ABySS (Assembly By Short Sequences) assembler is developed by Canada's Michael Smith Genome Science Centre.
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The short oligonucleotide analysis package (SOAP) is developed by BGI HK Research Institute in Hong Kong.
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The A5-miseq pipeline automates all the usual steps in genome assembly and is tuned to assemble microbial genomes from low coverage (<50x) Illumina data on laptop or desktop compute hardware. It was developed by Andrew Tritt and Aaron Darling.
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Meraculous2 is a scalable and efficient assembler geared for large eukaryotic genomes, developed by DOE Joint Genome Institute.
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Squeezamler is a divide-and-conquer algorithm for economical sequencing and assembly of all distinct genomes in a bacterial sample. The key idea here is exploiting sparsity, which is the small number of distinct genomes (~1000) in comparison to the huge number of cells (~100 trillion).
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Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. Minia is developed at the IRISA institute in France.
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De novo sequence assembler using string graphs developed at the Wellcome Trust Sanger Institute in the UK.
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MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner, it is developed in the department of Computer Science at the University of Hong Kong.
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SparseAssembler utilises a sparse k-mer graph structure evolved from the de Bruijn graph and is developed at the Chinese Academy of Sciences in Menglun.
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