Identify_chimera.py using usearch61: Confused about the output

[Shebl E Salem]

Hi all,

I ran the following commands to identify and filter chimera sequences from my data

identify_chimeric_seqs.py -i Ion13And14And15Combined.fna -m usearch61 -o usearch_checked_chimeras131415/ -r 97_otus.fasta

 

filter_fasta.py -f Ion13And14And15Combined.fna -o 131415seqs_chimeras_filtered.fna -s usearch_checked_chimeras131415/chimeras.txt -n

I am not sure if the chimeras.txt output from usearch61 contains chimeras detected by both denovo and reference based detection or not?

[Shebl E Salem]

Hi all,

I wonder if any one can help me with my previous questions (identify_chimeric_seqs.py using usearch61).

With my best wishes,

Shebl

[TonyWalters]

Hello Shebl,

The chimeras.txt file does contain the sequences flagged as chimeras both by usearch's reference and de novo methods.

[Shebl E Salem]

Hi Tony,

Thank you very much. I am so grateful to you.