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miga quality_wf and derep_wf not working for archaea genomes #157

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jianshu93 opened this issue Mar 21, 2023 · 1 comment
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miga quality_wf and derep_wf not working for archaea genomes #157

jianshu93 opened this issue Mar 21, 2023 · 1 comment
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1.4

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@jianshu93
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Hello Miguel,

I uploaded a archaea genome for testing purposes, which is an isolate archaea from Asgard phylum. It should be 100% complete.

I attached results from quality_wf and checkm:

completeness 28.8
contamination 1.8
quality 19.8

Bin Id Marker lineage # genomes # markers # marker sets 0 5+ Completeness Contamination Strain heterogeneity
Prometheoarchaeum_syntrophicum k__Archaea (UID2) 207 149 107 11 131 5 2 0 0 91.74 6.07 9.09

Prometheoarchaeum_syntrophicum.fasta.zip

Hope this can be fixed soon!

Many Thanks,

Jianshu
@jianshu93
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I am actually thinking on solution similar to that of checkm，using phylogenetic replacement to determine whether it is bacteria or archaea.

Thanks，

Jianshu

lmrodriguezr added a commit that referenced this issue Mar 21, 2023
@lmrodriguezr
Towards addressing #157
cb7c8c1 
Reduces the set of marker genes to those common between Archaea and Bacteria whenever taxonomy is not defined. It solves the most immediate issue with Archaea, but reduces precision for Bacteria. A more robust alternative would be to pre-annotate taxonomy (if missing) against Phyla_Lite
@lmrodriguezr lmrodriguezr modified the milestones: 1.3, 1.4 Apr 3, 2023
@lmrodriguezr lmrodriguezr mentioned this issue Apr 21, 2023
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