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Filter out contaminants as default #459

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adamcantor22 opened this issue Aug 11, 2023 · 0 comments
Open

Filter out contaminants as default #459

adamcantor22 opened this issue Aug 11, 2023 · 0 comments

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@adamcantor22
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adamcantor22 commented Aug 11, 2023

Is your feature request related to a problem? Please describe.
The following taxa (identified with the EISER project by Alba) should always be treated as contaminants:

  • Afipia
  • Aquabacterium
  • Asticcacaulis
  • Aurantimonas
  • Beijerinckia
  • Bosea
  • Bradyrhizobium
  • Brevundimonas
  • Caulobacter
  • Craurococcus
  • Devosia
  • Hoeflea
  • Mesorhizobium
  • Methylobacterium
  • Novosphingobium
  • Ochrobactrum
  • Paracoccus
  • Pedomicrobium
  • Phyllobacterium
  • Rhizobium
  • Sphingobium
  • Sphingomonas
  • Sphingopyxis
  • Acidovorax
  • Azoarcus
  • Azospira
  • Burkholderia
  • Curvibacter
  • Delftia
  • Duganella
  • Herbaspirillum
  • Janthinobacterium
  • Leptothrix
  • Limnobacter
  • Massilia
  • Methylophilus
  • Methyloversatilis
  • Pelomonas
  • Polaromonas
  • Ralstonia
  • Schlegelella
  • Sulfuritalea
  • Undibacterium
  • Variovorax
  • Enhydrobacter
  • Nevskia
  • Pseudoxanthomonas
  • Psychrobacter
  • Stenotrophomonas
  • Xanthomonas
  • Aeromicrobium
  • Arthrobacter
  • Beutenbergia
  • Brevibacterium
  • Tsukamurella
  • Abiotrophia
  • Brevibacillus
  • Brochothrix
  • Facklamia
  • Paenibacillus
  • Chryseobacterium
  • Dyadobacter
  • Flavobacterium
  • Hydrotalea
  • Niastella
  • Olivibacter
  • Pedobacter
  • Wautersiella
  • Deinococcus
  • Thermus
  • Tetragenococcus
  • Cellvibrio
  • Rhizobiales
  • Cyanobacteria
  • Streptophyta
  • Chloroplast
  • mitochondria
  • sapiens

Describe the solution you'd like
These taxa should be removed for all analyses, 16S and shotgun. This may require a custom script. Qiime2's qiime taxa filter command is basically broken, we can't be certain that just plugging these taxa into that command would have the desired effect.

Describe alternatives you've considered
We've mentioned decontam #412 in the past, could it help somehow? Are there other decontaminating tools available to us?

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