Ag3 cohorts analysis version 20240924

A new cohorts analysis version 20240924 has been released for the Ag3 data resource. This is now the default cohorts analysis version when using the malariagen_data Ag3 API. This cohorts analysis will be available for datasets up to and including Ag3.13.

Please note that the new cohorts analysis may change the values of sample metadata columns including taxon, admin1_iso, admin1_name, admin2_name, and derived columns beginning cohorts_ relative to previous cohorts analysis versions.

To pin this cohorts analysis when accessing data:

import malariagen_data

ag3 = malariagen_data.Ag3(
    cohorts_analysis="20240924",
)

This new version introduces some key changes:

• Samples previously labeled as gcx1 in the taxon field have been renamed to bissau:
  • gcx (gambiae complex cryptic taxa) labels serve as placeholders for groups outside our usual taxonomic assignment
  • Following Caputo et al. (2024), the gcx1 group has been renamed to Bissau molecular form
  • 291 samples previously assigned as gcx1, are now labeled as bissau.
  • 5 previously unassigned samples are also relabeled as bissau.
  • Cohort names have been updated, e.g. GM-M_gcx1_2019 is now GM-M_biss_2019

• 36 previously unassigned samples have been reclassified as: 32 melas, 2gambiae, 1 fontenillei, 1 arabiensis.

• A location metadata error affecting the administrative region (level 1) of 119 samples has been corrected:
  • admin1_iso updated from UG-E to KE-04
  • admin1_name updated from Eastern Region to Busia
  • Cohort names have been updated, e.g. UG-E_arab_2013 has now been relabeled to KE-04_arab_2013

If you need to access the previous version of the cohorts analysis, you can pin it using the code in here.