Reference-based chimera detection


1. UCHIME reference-based chimera detection

 

Using the EUKARYOME database for the reference-based chimera filtering process in usearch or vsearch (–uchime_ref):

 

vsearch --uchime_ref your_sequences.fasta 
--db EUK_SSU_tax_chim.fasta 
--nonchimeras nonchimeras.fasta

 

2. QIIME 2 reference-based chimera detection


Initially, you should change the format to the “.qza” format and import the files into QIIME 2:

 

#importing the taxonomy file:
qiime tools import --type 'FeatureData[Taxonomy]' 
--input-path EUK_SSU_tax_chim.tsv --output-path eukaryome_tax.qza

#importing the sequence
qiime tools import --input-path EUK_SSU_tax_chim.fasta 
--output-path eukaryome_seq.qza --type 'FeatureData[Sequence]'


QIIME 2 uses the VSEARCH plugin for reference-based chimera detection. Here’s how you can use it:
  

qiime vsearch uchime-ref 

--i-table table.qza 

--i-sequences your-seqs.qza 

--i-reference-sequences eukaryome_seq.qza 

--o-nonchimeras  nonchimeras.qza


It takes as input:

  • table.qza: The feature table was obtained from the sequence quality control step.

  • your-seqs.qza: The representative sequences obtained from the sequence quality control step.

  • eukaryome_seq.qza: A reference database of chimeric sequences

  • nonchimeras.qza: The output file where non-chimeric sequences will be stored

 

3. Mothur reference-based chimera detection

mothur provides the chimera.uchime command for reference-based chimera detection: 

mothur "#chimera.uchime(fasta=your_sequences.fasta, reference=EUK_SSU_tax_chim.fasta)"