Bonjour
Je suis ravi de rejoindre nextstrain.
J’ai une préoccupation. En effet j’ai soumis 157 séquences sur GISAID à partir du Burkina Faso mais au niveau de nextstrain je ne vois que 30 séquences. Pourriez vous m’aider à voir toutes les séquences.
Merci par avance pour ce que vous allez faire pour m’aider.
We can only display a fraction of the available sequences in a specific analysis. So from Burkina Faso only these 30
https://nextstrain.org/ncov/africa?f_country=Burkina%20Faso
make it into the build. But you could try to run your own analysis specific to Burkina Faso.
best,
richard
Hi,
Thank you for your reply
Why instead of 161 sequences you only show 30
best regards,
M. SAWADOGO Yacouba
Biologiste médical
Service de bactériologie virologie
CHU Sourô Sanou de Bobo Dioulasso.
Tel: (00226)70121792/78332809
we pick genomes over time from different countries so that we have a total of 2000 sequences from Africa. more recent genomes are given preference. This subsampling tries to make an interesting selection of viruses, but it also means that for a particular country it will only contain a fraction of the data.
Hi,
Thank you very much.
Now I understand you better.
Best regards
M. SAWADOGO Yacouba
Biologiste médical
Service de bactériologie virologie
CHU Sourô Sanou de Bobo Dioulasso.
Tel: (00226)70121792/78332809
Yacouba… je suggere que vous creer votre “Nextstrain build” locale a partir des sequences que avez. Avec le logiciel Nextstrain ca se fait facilement. Je pense que les membres de l’equip nextstrain pourrais vous aider avec le processus de l’installation et je pourrais aider avec la traduction des etapes si necessaire.
@rneher et l’equipe nextstrain sont les resources
Bryan Tegomoh
(bryan.tegomoh@gmail.com)
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Thank you for your reply.
I have some concerns and wanted to ask for your assistance again.
Indeed I wanted to have simple steps from the fast5 generated with a MinION to get the fastQ file and the fasta file. I am new to bioinformatics and wanted to be able to do these analyses.
Thank you in advance for your support.
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I’m just chiming in that I’m also a beginner that has been working on the same problem with relation to Haiti. Would it be useful to simply reproduce the same analysis as a reference for Burkini Faso, as a starting point?
@Yacsaw the pipelines discussed here produce phylogenetic analysis given finished consensus sequences. You seem to be looking for tools to build consensus sequences from raw reads. you might want to check here:
https://artic.network/ncov-2019
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