Plant de novo genome assembly of illumina reads on linux
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2.4 years ago

Hey, I am performing de novo genome assembly pipeline on plant illumina data. However, i have no idea if the tools used for plant specie for this purpose are same as for any other specie. Is there any reference de novo genome assembly pipeline available specific to plant illumina data? Kindly guide me in this regard.

I shall be very thankful for any help.

de_novo_genome_assembly linux plant_illumina_data • 1.3k views
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Apart from a few exceptions (for specific use-cases) I don't think there are assembler tools that are species dependent.

The process of assembly is equal for any given species (genome size might be the biggest factor here) and as such any assembler will assemble any genome.

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Okay many thanks

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2.4 years ago
liorglic ★ 1.4k

Usually assemblers aimed at eukaryotic genomes in general should work fine for plants. There are quite a few options, depending on the type and depth of sequencing data at hand, as well as the genome size and complexity and the available computational resources. Personally, I've tried SPAdes, which works well but only for small genomes, MEGAHIT, which is fast but in my experience results in lower N50, and the GATB Minia pipeline, which is the way to go if you are working on large (say >3Gb) genomes.

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Sure, thank you so much for your guidance.

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