Additional vector species added for IR and SpeciesID

[danieljbridges]

Aim is to ensure that all vector species for which NOMADS assays exist are directly supported. This PR adds the following genomes to nomadic:

• Anopheles stephensi
• Anopheles coluzzii
• Anopheles funestus
• Anopheles arabiensis
  Note that the underlying code for genome location downloads is already in nomadic - this PR simply exposes them to the end user.

Similarly, it does not add any new panels to nomadic, but rather applys the correct one to the above genomes, namely:

• NOMADS-IR - A panel developed to target key markers associated with insecticide resistance in three key vector species: An. funestus, An. gambiae and An. stephensi.
• NOMADS-SID - A panel targeting a set of genes that can be used to differentiate five different vector species: An. funestus, An. gambiae, An. stephensi, An. coluzzi and An. arabiensis

[JasonAHendry]

Hi @danieljbridges,

Thanks for initialising this, however we need different BED files for each of the species. Because the primers do not anneal to exactly the same positions across species, and the chromosomes are also named differently, the anopheles gambiae BED files will not work for the other species.

Note also we should have the insecticide resistance BED file for An. Arabiensis, rather than An. Funestus.

I can connect with Cynthia, as we had created BED files for each of the species we can add.

[danieljbridges]

Excellent points - was really just testing the downloads still worked (which they do). Have asked Cyprian to send for the other vectors for the SID panel as like Sylvia he must have generated them for mapping....

[berndbohmeier]

One comment to the bed files, maybe we also want to double check the names of each region, as we standardised them at some point for MVP, maybe we want to do here something similar.

[JasonAHendry]

I have located the BED files for the different species for the IR and SID panel. I generated them but it was two years ago so I would like to quickly review the approach before committing them to the main repository. I could add them to this pull request.

One point to note is that, for the SID application, the dashboard is less useful, as the primary need is mapping to multiple species. For IR this need can also arise, as there can be multiple species in a single experiment. We would have to decide whether we want to support such applications or not.

[danieljbridges]

Be great to add them in here, then we can test them with some real data and see that they are working as expected