Extracting the assemblies from wgs accessions

Question

[genomes_and_MGEs]

Hey everyone,

I just blasted a sequence against the wgs DB on NCBI. When I blast against the nt DB, I can import the accessions on Batch Entrez and directly fetch the assemblies. However, I can't do that when uploading the hits against the wgs DB. For example, I have these accession hits:

PJQP01000010.1 PJCO01000020.1 PJCN01000016.1 PESJ01000016.1 LKKS01000134.1 JFBC01000520.1 NEJN01000012.1 LQXW01000009.1 JWLN01000008.1 RJAI01000031.1 NTME01000046.1 MJVE01002323.1 LDPF01000101.1 JOJY01000001.1 AXUP01000411.1 ...

How can I extract the assemblies for all these accessions? Thank you guys! Cheers

Answer 1

[vkkodali_ncbi]

Batch Entrez is expecting a list of GIs. If you can get those somehow, you can use Batch Entrez. Alternately, assuming you want to download the sequences in FASTA format, you can use Entrez Direct for this as follows:

epost -input <accs_file> -db nuccore -format acc \
  | efetch -db nuccore -format fasta

where <accs_file> is a text file with accessions, one accession per line. You have options other than -format fasta; check them out in the documentation.