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NCBI Genome Download Sequence Report Indexing Sequences FNA file Tool Exist?

I'm looking to find an optimal global alignment for a coral genome to other mRNA sequences in other organisms. I pressed the download button to get the genome sequences(FASTA), Sequence Report(JSONL), and Assembly data report (JSONL). When it downloaded and I unzipped it. In data/GCA_025960835.1/sequence_report.jsonl it shows the different sequences and their information. I just want one of them but now I have to go get the file with the accession number or write a couple of functions to pull out the sequence I want. Is there a python solution to do this out the box that doesn't need much coding?

Thanks, David

fna json ncbi
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updated by Ram Ram • written by davidawarshawsky • davidawarshawsky

1 answer

While a python solution can be found this is easily achieved by using faSomeRecords tool from Jim Kent (UCSC) utilities. See more here: How do I extract Fasta Sequences based on a list of IDs?

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written by GenoMax GenoMax

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