Whole Genome Sequencing: Identification of genomic differences
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5 weeks ago
yiren • 0

hello everyone: Now ,I have a illumina whole genome seqence data of clinical fungal.I want to know the difference that my seqence from reference genome from NCBI.How can I do? thank you !

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Your question is lacking more detailed info to get meaningful answers. eg. What kind of differences are you looking for: large ones? snps? ... In any case the analysis you are looking for is : "variant calling" . Hence, that is what you would need to read up upon. This is nowadays a common analysis and several guidelines and tutorials are available for it. It is however far a to big of an analysis to here start explaining how you have to do it in practise.

If you have specific questions you're very welcome to post them on BioStars.

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thank you for your prompt reply.My question is that :how Can I find specify genome region in my genome refer to reference genome.Now ,I used bwa to map my fastq data to NCBI reference genome ,the mapping rate is 100% and I used gatk to call snps and indels ,then ,I found only 1000snps and 1400indel(the reference size is 12.5M).So ,my question is that my genome is same as reference genome?thank you very much .

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well, very strictly spoken no because there are still some variants apparently. Though the number is indeed quite low.

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thank you .Now ,I assembled the genome using SPAdes.what can I do for my genome sequence and the reference?Can I know the special region of two genomes respective and the similiary of the two genomes?Can you recommend some softwares ?

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