Finding the raw data used to build reference genomes
Is the a way to find the raw data (fastq or other) that was used to generate a reference genome? and is there a quick way to do this for a large number of genomes?
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You could do this using EntrezDirect. I am using random NCBI genbank assembly identifiers below. Once you have the SRA accession you can get at the sequence data.
$ esearch -db assembly -query GCA_008245085 | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -element Identifiers
BioSample: SAMN06711904; Sample name: PFDSM3638; SRA: SRS4513276
One more example (from RefSeq)
$ esearch -db assembly -query GCF_021347895 | elink -target biosample | efetch -format docsum | xtract -pattern DocumentSummary -element Identifiers
BioSample: SAMN16534234; Sample name: KAUSTApolyChrSc; SRA: SRS7576196
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