Obtain N50 stats from NCBI for all Hymenoptera genome assemblies

Question

[emeline.a.favreau]

Hello,

I would like to obtain scaffold N50 from all Hymenoptera genome assemblies found in NCBI page under Global statistics (e.g https://www.ncbi.nlm.nih.gov/assembly/GCF_000214255.1). Is there a way to quicky have access to these stats? I am looking for a dump-like command line.

Thanks in advance!

[microfuge]

I always find convinient to start with NCBI Taxonomy. One approach can be -

• In NCBI taxonomy https://www.ncbi.nlm.nih.gov/taxonomy enter Hymenoptera in search box
• Click on resulting link which opens this page https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=7399
• Check the Genome box in pink color, click GO
• The number of genomes in this clade is listed in Pink, click on it
• This redirects to NCBI genomes https://www.ncbi.nlm.nih.gov/genome/?term=txid7399[Organism:exp]
• In Find related data tab on right chooose Assembly from dropdown list then click find items
• There will be a blue box on top called "Download assemblies"
• Click on it and then for the file type choose Reports -> "Assembly statistics report"
• This should download All reports which contains L50 and N50

Answer 1

[vkkodali_ncbi]

You can use Entrez Direct for this as shown below:

esearch -db assembly -query 'txid7399[organism:exp]' \
  | esummary \
  | xtract -pattern DocumentSummary -element AssemblyAccession,AssemblyName,SpeciesTaxid,Organism,ContigN50,ScaffoldN50
GCA_000184785.2  Aflo_1.1                  7463     Apis florea (little honeybee)                        24915    2863240
GCA_009650705.1  Solenopsis_invicta_SB1.0  13686    Solenopsis invicta (red fire ant)                    945877   13114153
GCA_009602685.1  ASM960268v1               63436    Leptopilina heterotoma (wasps, ants, and bees)       9278     11848
GCA_009299975.1  ASM929997v1               13686    Solenopsis invicta (red fire ant)                    874937   16736736
GCA_009299965.1  ASM929996v1               13686    Solenopsis invicta (red fire ant)                    278331   11613644

[microfuge]

Really liked this solution!

[emeline.a.favreau]

I used this and it was perfect for my needs. Now I also want the date of the assembly. I tried the following but the resulting file was the same as your result (ie no column for the date). Do you know how I could do this?

esearch -db assembly -query 'txid7399[organism:exp]' \
  | esummary \
  | xtract -pattern DocumentSummary -element AssemblyAccession,Date,AssemblyName,SpeciesTaxid,Organism,ContigN50,ScaffoldN50

[vkkodali_ncbi]

You need to provide the complete element name, for example AsmReleaseDate_RefSeq, as shown below:

esearch -db assembly -query 'txid7399[organism:exp]' \
  | esummary \
  | xtract -pattern DocumentSummary -element AssemblyAccession,AsmReleaseDate_RefSeq,AssemblyName,SpeciesTaxid,Organism,ContigN50,ScaffoldN50
GCA_010883055.1 1/01/01 00:00   B_treatae_v1    1159321 Belonocnema treatae (wasps, ants, and bees)     19588   150973230
GCA_010645185.1 1/01/01 00:00   Tetragonula_hockingsi_1.1       270528  Tetragonula hockingsi (bees)    10501   10501
GCA_010645165.1 1/01/01 00:00   Tetragonula_davenporti_1.1      597209  Tetragonula davenporti (bees)   18510   18510
GCA_010645135.1 1/01/01 00:00   Tetragonula_clypearis_1.1       270525  Tetragonula clypearis (bees)    14852   14852