How to use Vsearch

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T A

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Aug 11, 2017, 3:24:02 AM8/11/17
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Hello 
I am a graduated student .
I am sorry. I'm not good at English.
I want to use vsearch.
But I can not understand vsearch.

What I want to do with vsearch

※with usearch
①time identify_chimeric_seqs.py -i AAA.fna -m usearch61 -o chimera_usearch -r ../../gg_13_8_otus/rep_set/97_otus.fasta

②filter_fasta.py -f AAA.fna -o seqs_filtered.fna -s chimera_usearch/non_chimeras.txt

③pick_open_reference_otus.py -i seqs_filtered.fna -o open_ref_otu -r ../../gg_13_8_otus/rep_set/97_otus.fasta -p ../../Script/uc_fasta_params.txt

④sort_otu_table.py -i open_ref_otu/otu_table_mc2_w_tax_no_pynast_failures.biom -o sorted_otu_table.biom

I think
①=vsearch --uchime_ref fastafile --nonchimeras outputfile:BBB --db fastafile [options]

Should I give outputfile extension?

I don`t understand ②〜 with vsearch.

please help me.

Jose Antonio Navas Molina

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Aug 11, 2017, 10:35:25 AM8/11/17
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Hi TA,

For specific questions about Vsearch I would contact the developers of vsearch directly in their forum.

For steps 2 and 4 vsearch/usearch is not needed so you can run them with the specific vsearch files.

For step 3, pick_open_reference_otus.py it's a workflow script that executed multiple steps. It performs multiple calls to usearch so replicating it's behavior may be a bit more complex. If I recall correctly, vsearch was designed to be a drop-in replacement of usearch, so you may be ok to alias vsearch as usearch61 and it may work. However, I know small differences exists in the interface of the two programs, but the vsearch developers will have a higher insight.

May be some other more experienced vsearch users can "qiime" in and provide a bit more insight.

Cheers,

T A

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Aug 12, 2017, 11:04:32 AM8/12/17
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Hi Jose Antonio Navas Molina

Thank you for your prompt response.

I will try.
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