Tool:A resource with diverse databases and tools for SARS-CoV-2 (COVID-19) bioinformatics -- Updates

Question

[Michael]

Dear bioinformatics and genomics community

We are in the process of setting up resources helpful for bioinformatics/genomics analyses related to SARS-CoV-2 (COVID-19).

So far we offer the following databases/tools on our website:

• Up to date Centrifuge database including SARS-CoV-2 genome (including prokaryotes, viruses and human genome)
• EDIT: We added a Kraken2 database with Viral genome plus Human including SARS-CoV-2
• EDIT: We added a MetaMaps database "human and viral" including 88 SARS-CoV-2 genomes
• Database with kmers specific for SARS-CoV-2 (from 19bp to 25 bp) based on 89 SARS-CoV-2 genomes and extensive check for off-targets
• Database with kmers found in 89 (EDIT: Now 153) SARS-CoV-2 genomes examined (but not exclusively in SARS-CoV-2, in contrast to the specific kmers mentioned above)
• Multiple sequence alignment (MSA) of all public complete SARS-CoV-2 genome assemblies(n=93 EDIT: Now 102)
• Consensus based on MSA of 102 complete genomes
• All complete SARS-CoV-2 genomes as one FASTA file (n=93 EDIT: Now 102). Yes, this is pretty trivial to generate, but some people might not be very familiar with NCBI's Databases.

We are currently extending our resources with new databases/tools and at the same time are working on improving the resources mentioned above.

Please visit https://genexa.ch/sars2-bioinformatics-resources/

Please be aware that this is work in progress and if something is missing or not finished check again in a couple of hours. This is an effort to rapidly provide the community with tools related to SARS-CoV-2 genomics and bioinformatics. We really hope it turns out to be helpful!

If you want to help, please send a mail to the contact mentioned on the website.

Tell us what you miss and what you think can be improved.

Best regards,
Michael

UPDATES:

• UPDATE1: We now added Centrifuge database "human+virus RefSeq" including SARS-CoV-2
• UPDATE2: We added Kraken2 database "human+virus RefSeq" including SARS-CoV-2
• UPDATE3: We added more genomes to the kmer analysis (21th March 2020)
• UPDATE4: We provide the 100 complete genomes used in the kmer analysis as one FASTA, 93 from NCBI GenBank, 7 from Chines National GenBank
• UPDATE5: We now added Centrifuge database "human+PROKARYOTES+virus RefSeq" including SARS-CoV-2
• UPDATE6: More complete genomes added to MSA and for download
• UPDATE7: We added a MetaMaps database "human + viral"
• UPDATE8: We added more genomes to the kmer analysis (n=153) (29th March 2020)

[GenoMax]

SARS-CoV-2 is the official name of this virus. Correct on your website but not in this post.

[Michael]

Sure, I was sometimes shortening it on the resources page but will adjust it here.

[Istvan Albert]

Thanks for putting this together.

The real shame is that GISAID still locks away genomic the data behind a phony registration window and extremely restrictive licensing.

We need to call on the German government to immediately stop the practice. I am going to make a new post on it.

[Michael]

Cool, thanks for the petition!

I am actually trying to get a hold on the GISAID assemblies and integrate it into analyses where the actual sequence is not directly visible. This should be fine I guess.

[Istvan Albert]

yes exactly, mention this on the petition thread.

I have known about the GISAID practice for a while now, reading about your resource made me realize that you like many others are restricted from doing all that you can

EDIT: you just did. great!