<p>According to the <a href="https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch_manual.pdf" rel="nofollow noreferrer">VSEARCH docs</a>, since you have specified <code>--sizeout</code> your abundances have been written into the FASTA headers:</p>
<blockquote>
<p>--sizeout</p>
<p>Take into account the abundance annotations present in the input fasta file (search for the pattern ’[&gt;;]size=integer[;]’ in sequence headers). That option is active by default when rereplicating.</p>
<p><strong>Add abundance annotations to the output fasta file (add the pattern ’;size=integer;’ to sequence headers).</strong> If --sizein is specified, each unique sequence receives a new abun- dance value corresponding to its total abundance (sum of the abundances of its occur- rences). If --sizein is not specified, input abundances are set to 1, and each unique sequence receives a new abundance value corresponding to its number of occurrences in the input file.</p>
</blockquote>

CC BY-SA 4.0
2020-11-27T20:53:21.960Z
2020-11-27T20:53:21.960Z
Maximilian Press
<p>I am working on a project and used the following command:</p>
<pre><code>vsearch --derep_fulllength filtered_merged.fa -sizeout -relabel Uniq -output dereplicated_filtered_merged.fa
</code></pre>
<p>and got the following output:</p>
<pre><code>87373926 nt in 203453 seqs, min 310, max 480, avg 352
Sorting 100%
10981 unique sequences, avg cluster 2.0, median 1, max 1287
Writing output file 100% 
</code></pre>
<p>The output had provided me with the data that 10981 unique sequences have been identified. But I cant seem to identify how many reads of the most common sequence were present in the input data.</p>
<p>Any suggestions will be kindly appreciated!</p>

CC BY-SA 4.0
2020-11-27T20:50:13.070Z
Can you post a sample of the output fasta? According to the VSEARCH docs the abundance information should be contained there (https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch_manual.pdf).
Maximilian Press
<fasta><clustering><metagenome>
Metagenomics: Identifying most common sequences
# Metagenomics: Identifying most common sequences

(Asked by: username_0 on 2020-11-27)

I am working on a project and used the following command:
vsearch --derep_fulllength filtered_merged.fa -sizeout -relabel Uniq -output dereplicated_filtered_merged.fa

and got the following output:
87373926 nt in 203453 seqs, min 310, max 480, avg 352
Sorting 100%
10981 unique sequences, avg cluster 2.0, median 1, max 1287
Writing output file 100% 

The output had provided me with the data that 10981 unique sequences have been identified. But I cant seem to identify how many reads of the most common sequence were present in the input data.
Any suggestions will be kindly appreciated!

**Tags:** fasta, clustering, metagenome
> **Comments:**
> **username_1**: Can you post a sample of the output fasta? According to the VSEARCH docs the abundance information should be contained there (https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch_manual.pdf).  

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## 1 answers

### Answer by username_1 on 2020-11-27. Score: 1 | Accepted answer

According to the [VSEARCH docs](https://github.com/torognes/vsearch/releases/download/v2.15.1/vsearch_manual.pdf), since you have specified `--sizeout` your abundances have been written into the FASTA headers:

> --sizeout
>
> Take into account the abundance annotations present in the input fasta file (search for the pattern ’[>;]size=integer[;]’ in sequence headers). That option is active by default when rereplicating.
>
> **Add abundance annotations to the output fasta file (add the pattern ’;size=integer;’ to sequence headers).** If --sizein is specified, each unique sequence receives a new abun- dance value corresponding to its total abundance (sum of the abundances of its occur- rences). If --sizein is not specified, input abundances are set to 1, and each unique sequence receives a new abundance value corresponding to its number of occurrences in the input file.


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