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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?
The text was updated successfully, but these errors were encountered:
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:
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?
The text was updated successfully, but these errors were encountered: