<p>My personal approach to something like this is to first try to reproduce existing work in order to learn to use relevant tools and understand the concepts involved. Then as you get more comfortable with the subject matter, you may spot an opportunity to add value. </p>

<p>If you'd like to get started with the phylogenomics side of things, you can use this public workspace developed by the viral genomics group at the Broad Institute, which includes viral genome sequences from NCBI SRA as well as some workflows for doing genome assembly and quality control: <a href="https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19" rel="nofollow noreferrer">https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19</a></p>

CC BY-SA 4.0
2020-04-23T19:09:04.403Z
FWIW we recently updated the viral genome assembly workflow and added a workflow for running Augur (from NextStrain) to do the phylogenomic analysis of multiple strains.
Geraldine_VdAuwera
CC BY-SA 4.0
2020-04-08T14:54:15.687Z
2020-04-08T17:52:42.407Z
2020-04-08T17:52:42.407Z
Geraldine_VdAuwera
<p>Please note that Cuvid19 is COVID-19, the WHO nomenclature. SARS2 is specifically called SARS-CoV-2 and is the virologists name for COVID-19 because that is the nomenclature of the International Committee on the Taxonomy of Viruses (ICTV) for the same virus following formal taxonomic investigation. It is important not to get the names confused.</p>

<p>Technically you are asking to compare COVID-19 with COVID-19. Whilst that is a standard investigation this would be technically rewritten "to investigate the molecular epidemiology of COVID-19".  If you are working within the virological community then the virus is termed SARS2-CoV-2. Phylogeny is a key approach, rather than "comparative genomics".</p>

<p>I wish you luck with your study. </p>

CC BY-SA 4.0
2020-11-24T20:13:55.007Z
SARS2 and  SARS-CoV-2 would be the names of the virus (as synonyms). COVID-19 is the name of the patology, the name of illness
RosLuP
CC BY-SA 4.0
2020-04-09T12:06:50.820Z
Dear Thank you, so you suggest after sequencing and assembly, I construct a phylogenetic tree
M.Bioinfo
CC BY-SA 4.0
2020-04-08T20:37:45.110Z
2020-04-08T20:45:03.127Z
2020-04-08T20:45:03.127Z
M__
<p>Dear Researches community </p>

<p>A question concerning the current outbreak, recently we attempting to contribute to the study of the Covid19, with a tight submission time ( 4 weeks).</p>

<p>Inquiring help because I'm not a virologist with an insufficient biological background. However, I assume able to do in silico analysis or ( dry lab). 
Moreover, <strong>new sample</strong> sequences from local <strong>strain</strong> will be provided. Assembly and annotation could be done at the first stage. Then perhaps a comparative genome investigation between the old SARS and the Cuvid19.</p>

<p>Furthermore, The virus estimation length that causes all this is only around 29,829 base pairs of RNA. The genome contains at least 10 predicted open reading frames (ORFs): ORF1a,  ORF1b, S,  3,  4a, 4b,  5,  E,  M  and  N,  with sixteen predicted nonstructural proteins being encoded by ORF1a/b. 
I am wondering if someone can assist by considering a particular section to focus on or a study suggests. Perhaps we can contribute at least 0.001 % to the communities.</p>

<p>I have been reading articles around, and seems are thousand of them every day.</p>

<p>so I have come up with starting list:</p>

<ol>
<li>Genome assemblies, annotation</li>
<li>epitome studies
Here you predict the protein sequences based on the genome that will sequence, then there are a number of tools that analyze the immunogenicity of different proteins
That can help you identify parts of the COVID-19 proteins that are likely to be detected by the immune system and they, of course, can be targeted by vaccine developers.</li>
<li>comparison between old saras Vs newCoVID</li>
<li>The M protein is a good target. It is extremely abundant in the nucleocapsid and is the protein responsible for giving the virus it's the shape, Almost everyone is looking at the S protein, which is justified. But there is not as much focus on the M protein.</li>
</ol>

<p>Your response is highly appreciated if you could attach the any reference related to the list above.</p>

CC BY-SA 4.0
2020-04-08T20:42:57.530Z
I would advise editting your question, firstly grammar (it is difficult understand) and then to a technical question. One vote for closure has already been initiated (not by me). At present you are outside the remit of the site for asking a question.
M__
CC BY-SA 4.0
2020-04-09T11:37:43.840Z
It is bioinformatics community where we all exchange ideas, students, doctors, researchers if you don't have an answer, please escape the page and keep the comment to your self @ATpoint
M.Bioinfo
CC BY-SA 4.0
2020-04-09T11:40:08.660Z
@Michael  An apology dear for my writing, excuse my language it's not my mother tongue still learning :(, anyway thank you I have edited again I hope looks better
M.Bioinfo
<covid-19><literature-search>
Concerning the current outbreak, using bioinformatics
# Concerning the current outbreak, using bioinformatics

(Asked by: username_0 on 2020-04-08)

Dear Researches community

A question concerning the current outbreak, recently we attempting to contribute to the study of the Covid19, with a tight submission time ( 4 weeks).

Inquiring help because I'm not a virologist with an insufficient biological background. However, I assume able to do in silico analysis or ( dry lab).
Moreover, **new sample** sequences from local **strain** will be provided. Assembly and annotation could be done at the first stage. Then perhaps a comparative genome investigation between the old SARS and the Cuvid19.

Furthermore, The virus estimation length that causes all this is only around 29,829 base pairs of RNA. The genome contains at least 10 predicted open reading frames (ORFs): ORF1a, ORF1b, S, 3, 4a, 4b, 5, E, M and N, with sixteen predicted nonstructural proteins being encoded by ORF1a/b.
I am wondering if someone can assist by considering a particular section to focus on or a study suggests. Perhaps we can contribute at least 0.001 % to the communities.

I have been reading articles around, and seems are thousand of them every day.

so I have come up with starting list:

1. Genome assemblies, annotation
2. epitome studies
   Here you predict the protein sequences based on the genome that will sequence, then there are a number of tools that analyze the immunogenicity of different proteins
   That can help you identify parts of the COVID-19 proteins that are likely to be detected by the immune system and they, of course, can be targeted by vaccine developers.
3. comparison between old saras Vs newCoVID
4. The M protein is a good target. It is extremely abundant in the nucleocapsid and is the protein responsible for giving the virus it's the shape, Almost everyone is looking at the S protein, which is justified. But there is not as much focus on the M protein.

Your response is highly appreciated if you could attach the any reference related to the list above.

**Tags:** covid-19, literature-search
> **Comments:**
> **username_1**: I would advise editting your question, firstly grammar (it is difficult understand) and then to a technical question. One vote for closure has already been initiated (not by me). At present you are outside the remit of the site for asking a question.  
> **username_0**: It is bioinformatics community where we all exchange ideas, students, doctors, researchers if you don't have an answer, please escape the page and keep the comment to your self @ATpoint  
> **username_0**: @Michael  An apology dear for my writing, excuse my language it's not my mother tongue still learning :(, anyway thank you I have edited again I hope looks better  

---

## 2 answers

### Answer by username_2 on 2020-04-08. Score: 4

My personal approach to something like this is to first try to reproduce existing work in order to learn to use relevant tools and understand the concepts involved. Then as you get more comfortable with the subject matter, you may spot an opportunity to add value.

If you'd like to get started with the phylogenomics side of things, you can use this public workspace developed by the viral genomics group at the Broad Institute, which includes viral genome sequences from NCBI SRA as well as some workflows for doing genome assembly and quality control: <https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19>

> **Comments:**
> **username_2**: FWIW we recently updated the viral genome assembly workflow and added a workflow for running Augur (from NextStrain) to do the phylogenomic analysis of multiple strains.  

---

### Answer by username_1 on 2020-04-08. Score: 2

Please note that Cuvid19 is COVID-19, the WHO nomenclature. SARS2 is specifically called SARS-CoV-2 and is the virologists name for COVID-19 because that is the nomenclature of the International Committee on the Taxonomy of Viruses (ICTV) for the same virus following formal taxonomic investigation. It is important not to get the names confused.

Technically you are asking to compare COVID-19 with COVID-19. Whilst that is a standard investigation this would be technically rewritten "to investigate the molecular epidemiology of COVID-19". If you are working within the virological community then the virus is termed SARS2-CoV-2. Phylogeny is a key approach, rather than "comparative genomics".

I wish you luck with your study.

> **Comments:**
> **username_0**: Dear Thank you, so you suggest after sequencing and assembly, I construct a phylogenetic tree  
> **username_3**: SARS2 and  SARS-CoV-2 would be the names of the virus (as synonyms). COVID-19 is the name of the patology, the name of illness  

---

