Download LKAM01

[sjackman]

Is there an option to download assembly LKAM01 Picea glauca (white spruce) mitochondrial, whole genome shotgun sequence?
https://www.ncbi.nlm.nih.gov/nuccore/?term=LKAM01
ftp://ftp.ncbi.nlm.nih.gov/sra/wgs_aux/LK/AM/LKAM01/LKAM01.1.fsa_nt.gz

❯❯❯ ncbi-genome-download -A LKAM01 -F fasta all
ERROR: No downloads matched your filter. Please check your options.

[sjackman]

Could there be an option to download all mitochondrial or plastid genomes of a given taxa?

[kblin]

ncbi-genome-download doesn't do SRA downloads, just GenBank and RefSeq. It also doesn't know about taxonomy apart from what's in the assembly summary text file. The gimme_taxa.py script in contrib can find taxids to filter for, but also doesn't know about what entries are mitochondrial/plastid.

[kblin]

That said, https://www.ncbi.nlm.nih.gov/nuccore/LKAM00000000.1 seems to be the WGS master record for it, and I'm planning to add WGS support to ncbi-acc-download soon, so that might be an option once you know the ID.

[sjackman]

I'm planning to add WGS support to ncbi-acc-download soon, so that might be an option once you know the ID.

Excellent! I look forward to that feature.

[kblin]

I forgot about this question for a bit, sorry. Current versions of https://github.com/kblin/ncbi-acc-download/ support recursive downloads to grab WGS entries.

[sjackman]

Yeah! Thanks, Kai.

[tseemann]

@sjackman ncbi-acc-download -v --recursive LKAM00000000.1 seems to work.
Close this issue?