This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Retrieving assembly statistics for several accessions

Hey everyone,

I would like to download the global statistics for several assemblies. For example, on this link https://www.ncbi.nlm.nih.gov/assembly/GCF_000159415.1/, you can see the Global Statistics (sequence length, N50, number of contigs, etc.). I have a list of RefSeq accessions, like the one down:

GCF_000014425.1 GCF_000056065.1 GCF_000155915.2 GCF_000159335.1 GCF_000159355.1 GCF_000159415.1 GCF_000160855.1 GCF_000160875.1

Is it possible to extract Global Statistics for several RefSeq accessions? Probably using Entrez Direct. Cheers

assembly sequence genome
• 1,213 views • link
written by genomes_and_MGEs • genomes_and_MGEs

1 answer

using a XML transformation with xslt+xsltproc:

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks man! This is very helpful. I would like to show this data in a table. For example, first colum with descriptio, 2nd with sequence length, 3rd with no. of contigs, etc. Could you please let me know out to do that? Thanks!

• 0 views • link
written by genomes_and_MGEs • genomes_and_MGEs

Log in to answer this question.

More posts like this