NCBI has two sections for assemblies, genbank (all submitted sequences) and RefSeq (curated genbank sequences).
A list of both is available here:
ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/assembly_summary_refseq.txt
and ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/assembly_summary_genbank.txt.
Now I want to get a list of assembly (genome) accession numbers, that are in genbank but not in RefSeq. Unfortunately I could not find any mapping file on NCBI's sites. Has someone an idea how to obtain that list?
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written
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rororo •
1 answer
The assembly_summary_genbank.txt file has a field gbrs_paired_asm which indicates whether there is a matched RefSeq pair for a given GenBank assembly. You should be able to get the entire list of assemblies without a matching RefSeq assembly as follows:
awk 'BEGIN{FS="\t";OFS="\t"}($18=="na")' assembly_summary_genbank.txt
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Unless I'm missing a trick, this should be as simple as something like:
Haven't double checked that this is 100% accurate though, and assumes I got the files the right way round!