File to use when chimera checking with vsearch

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nlh15

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Jul 9, 2016, 1:49:11 PM7/9/16
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Hello all,

I know other people have touched on the subject, however my question is a bit different and fairly simple.
I have clustered my data set with the script pick_open_reference_otus.py and the next step for me is to chimera check via vsearch. I have tried the denovo version and found it to be extremely time-consuming in the case of my extensive data set so I am trying to use the reference version. My question is which one of the files from the clustering output is the one to use as input file when chimera checking. This is the output in my clustering directory:

3125CSS_normalized_otu_table.biom  otu_table_mc2_w_tax.biom
3125_norm_derepref.txt             otu_table_mc2_w_tax_no_pynast_failures.biom
chimeric_vsearchderep.fasta        otu_table_non_chimeric.biom
derep_rep_set.fasta                pynast_aligned_seqs
final_otu_map_mc2.txt              rep_set.fna
final_otu_map.txt                  rep_set.tre
index.html                         step1_otus
log_20160630153747.txt             step2_otus
new_refseqs.fna                    step3_otus
nonchimeric_vsearchderep.fasta     step4_otus
otu_table_mc2.biom                 uclust_assigned_taxonomy

Chimera slayer requires the pynast aligned file but vsearch wants a file that has all of the otus in it so it can later be dereplicated and abundance information added to it.
This may seem like a silly question and I am okay with a silly answer as long as it is accurate!

Thank you

// Nine

zhiying Guo

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Jul 9, 2016, 9:21:07 PM7/9/16
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Hello,

Use the final representative sequence (rep_set.fna) file as input of Vsearch to do reference-based chimera check.
However, if you process the data is this way, there should be a condition that chimera and non-chimera cluster independent OTUs.
You can also read this post for more information.

Hope it helps
Best,
Zhiying Guo

AS

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May 18, 2021, 11:51:54 PM5/18/21
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Can someone please tell me if de-novo chimera checking using vsearch can be conducted on representative sequences generated after picking OTUs with sumaclust?
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