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improving genome sequence read depth and confidence by combining sequences from different SRA

Hi all, I have a genome sequenced with not so good coverage. so i am thinking of utilizing other available genomes to develop a complete draft genome. I am also thinking of incorporation of transcriptomics reads to further improve the confidence. can i have suggestions on pros and cons of this trick. and also beginner suggestions of tools that i can use.

transcriptome genomics ngs
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updated by Jautis Jautis • written by Tenacious aim • Tenacious aim

2 answers

You can make an assembly using reads from different specimens of the same species, but only if the intraspecific polymorphism is not too large. What "too large" means is a complicated question. If I were you, I would try.

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written by shelkmike shelkmike

Yes, you can combine sequences from multiple individuals, but keep in mind that genetic variation can make it difficult to form a consensus sequence and you may need to remove highly similar contigs which presumably represent the same region in multiple individuals

Also, transcriptomes typically aren't that helpful for eukaryotic genome assembly because of splicing. They are helpful for gene annotation once you have an assembly!

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written by Jautis Jautis

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