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Welcome to the VSEARCH Forum!

This group is intended for discussions about the open source metagenomics tool VSEARCH available at https://github.com/torognes/vsearch

You are welcome to ask questions, answer questions, report bugs, suggest features to be added, or just about anything related to VSEARCH.

If you would like to report bugs or suggest new features, we would prefer that these are submitted as issues on the Github site: https://github.com/torognes/vsearch/issues

Due to recent spam, the group is now moderated. To be accepted as a member, please describe your scientific work briefly in one sentence to show that you are a not a spammer.

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Sep 18

Pac Bio amplicon clustering

Dear vsearch community, I have a question regarding PacBio amplicon read processing using vsearch.

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Pac Bio amplicon clustering

Dear vsearch community, I have a question regarding PacBio amplicon read processing using vsearch.

Sep 18

Marita White, Colin J Brislawn5

Aug 4

ASVs vs 97% OTUs when using -usearch_global to create an OTU table

Makes sense, thanks! On Tuesday, July 29, 2025 at 7:41:55 PM UTC-7 Colin J Brislawn wrote: Another

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ASVs vs 97% OTUs when using -usearch_global to create an OTU table

Makes sense, thanks! On Tuesday, July 29, 2025 at 7:41:55 PM UTC-7 Colin J Brislawn wrote: Another

Aug 4

Ashley Paulsen, … torognes5

Jan 31

Recommendations for clustering ONT reads with variable length?

Hi I have a few recommendations regarding Nanopore reads. The first is to lower the gap open penalty

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Recommendations for clustering ONT reads with variable length?

Hi I have a few recommendations regarding Nanopore reads. The first is to lower the gap open penalty

Jan 31

Karen Daiana Schoninger, Frédéric Mahé2

12/17/24

Cluster different samples, I need same otus id

Hello Karen, if I am not mistaken, you've posted a similar question on GitHub (https://github.com

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Cluster different samples, I need same otus id

Hello Karen, if I am not mistaken, you've posted a similar question on GitHub (https://github.com

12/17/24

ekar...@gmail.com, Torbjørn Rognes3

8/6/24

Max length for derep or cluster commands

Thank you. On Tuesday, August 6, 2024 at 11:02:12 AM UTC+2 Torbjørn Rognes wrote: Hi There is no hard

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Max length for derep or cluster commands

Thank you. On Tuesday, August 6, 2024 at 11:02:12 AM UTC+2 Torbjørn Rognes wrote: Hi There is no hard

8/6/24

7/10/24

How to analyze several fastq files at once + Other Questions

I'm using VSEARCH for the first time and am having trouble with two things: i) selecting all of

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How to analyze several fastq files at once + Other Questions

I'm using VSEARCH for the first time and am having trouble with two things: i) selecting all of

7/10/24

7/3/24

More OTU counts than number of starting/merged reads in a sample

Hi, Is it normal to have a higher number of read counts in a sample where initially the raw reads

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More OTU counts than number of starting/merged reads in a sample

Hi, Is it normal to have a higher number of read counts in a sample where initially the raw reads

7/3/24

Marita White, … Frédéric Mahé4

6/27/24

OTU Table Labels

Thanks both of you for your helpful and quick replies! I ended up adding the --sample option to my

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OTU Table Labels

Thanks both of you for your helpful and quick replies! I ended up adding the --sample option to my

6/27/24

Mushahid Shamim, … Frédéric Mahé4

12/20/23

Is the usearch --otutab and vsearch --usearch_global command is same

Hi @Colin, I am not getting any error. Its just produce empty file which means no OTUs can be matched

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Is the usearch --otutab and vsearch --usearch_global command is same

Hi @Colin, I am not getting any error. Its just produce empty file which means no OTUs can be matched

12/20/23

gbbio, … Frédéric Mahé4

11/23/23

vsearch --usearch_global N streches

@Colin J Brislawn Oh thanks! I was never aware of the manual. @Frédéric Mahé I am not sure about your

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vsearch --usearch_global N streches

@Colin J Brislawn Oh thanks! I was never aware of the manual. @Frédéric Mahé I am not sure about your

11/23/23

Emily Van Syoc, … Frédéric Mahé7

10/31/23

--uchime_denovo doesn't write nonchimeras using abundance information

Great, thank you! On Monday, October 30, 2023 at 11:29:08 AM UTC-4 Frédéric Mahé wrote: Here is a toy

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--uchime_denovo doesn't write nonchimeras using abundance information

Great, thank you! On Monday, October 30, 2023 at 11:29:08 AM UTC-4 Frédéric Mahé wrote: Here is a toy

10/31/23

Hu Peiyao, … Frédéric Mahé6

10/17/23

Inconsistent reads between derep.fa and otutab?

I got it, Thanks a lot! On Tuesday, October 17, 2023 at 10:10:47 PM UTC+8 Frédéric Mahé wrote:

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Inconsistent reads between derep.fa and otutab?

I got it, Thanks a lot! On Tuesday, October 17, 2023 at 10:10:47 PM UTC+8 Frédéric Mahé wrote:

10/17/23

Rita Domingues, Colin J Brislawn2

10/11/23

Hello! Hopefully you have found the answers already, but if not, here's how I would address these

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Hello! Hopefully you have found the answers already, but if not, here's how I would address these

10/11/23

ekar...@gmail.com, … Colin J Brislawn4

8/13/23

Merged unsync fastq files

Thank you, Torbjørn and Colin. On Saturday, August 12, 2023 at 8:27:11 AM UTC+2 cbr...@gmail.com

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Merged unsync fastq files

Thank you, Torbjørn and Colin. On Saturday, August 12, 2023 at 8:27:11 AM UTC+2 cbr...@gmail.com

8/13/23

Érico Polo, Torbjørn Rognes2

5/31/23

fastq_mergepairs: multiple potential alignments report

Hi Thanks for the feedback. There is no way to get this information today, but I have added an issue

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fastq_mergepairs: multiple potential alignments report

Hi Thanks for the feedback. There is no way to get this information today, but I have added an issue

5/31/23

5/22/23

23S and 16S analysis

It's my first time with VSEARCH. I've been testing commands but they aren't giving me

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23S and 16S analysis

It's my first time with VSEARCH. I've been testing commands but they aren't giving me

5/22/23

4/26/23

replacing perl script with shell command line

I have found an alternate map.pl script that works: https://github.com/telatin/vsearch_example/blob/

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replacing perl script with shell command line

I have found an alternate map.pl script that works: https://github.com/telatin/vsearch_example/blob/

4/26/23

Duan Copeland, … Colin Brislawn5

11/9/22

mothur output file is too large

>--mothur_shared_out newmeta.original.shared is the 533 GB file from my --usearch_global command

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mothur output file is too large

>--mothur_shared_out newmeta.original.shared is the 533 GB file from my --usearch_global command

11/9/22

tima...@gmail.com, … Torbjørn Rognes5

10/10/22

Problem: vsearch fastq_mergepairs gives drastically different results than usearch

Hi The merge_pairs function initially looks for shared k-mers by the R1 and R2 reads in the

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Problem: vsearch fastq_mergepairs gives drastically different results than usearch

Hi The merge_pairs function initially looks for shared k-mers by the R1 and R2 reads in the

10/10/22

Hu Peiyao, Frédéric Mahé2

8/31/22

Vsearch cluster results seems inconsistent

Hello, clustering results can vary for obvious reasons: - different command-line parameters, -

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Vsearch cluster results seems inconsistent

Hello, clustering results can vary for obvious reasons: - different command-line parameters, -

8/31/22

Stephanie Schnorr, Torbjørn Rognes5

1/11/22

Dereplication with fastq out file

Fantastic, thanks so much for creating and implementing this feature! On Monday, January 10, 2022 at

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Dereplication with fastq out file

Fantastic, thanks so much for creating and implementing this feature! On Monday, January 10, 2022 at

1/11/22

Francesca Lioce, Torbjørn Rognes2

12/14/21

micca otu vsearch error

Hi It is not possible to see from the message what the error is. It appears to have terminated after

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micca otu vsearch error

Hi It is not possible to see from the message what the error is. It appears to have terminated after

12/14/21

12/8/21

different otu numbers in otu table and rep seqs

Hi all, I found the numbers of otus between my feature table and rep seqs file are different. There

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different otu numbers in otu table and rep seqs

Hi all, I found the numbers of otus between my feature table and rep seqs file are different. There

12/8/21

Kevin Wamae, … Torbjørn Rognes5

5/4/21

usearch_global not matching even at lower identity

Thanks Torbjørn for pointing that out. I think if vsearch would automatically adjust these parameters

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usearch_global not matching even at lower identity

Thanks Torbjørn for pointing that out. I think if vsearch would automatically adjust these parameters

5/4/21

Marcel Zandberg, Frédéric Mahé3

4/15/21

Reference database

Thanks Frédéric Mahé, That was exactly what I meant. It works like a charm Op donderdag 15 april 2021

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Reference database

Thanks Frédéric Mahé, That was exactly what I meant. It works like a charm Op donderdag 15 april 2021

4/15/21

Nayla Abney, … Frédéric Mahé5

3/7/21

Unrecognized string Error

Hi Nayla, the error message concerns your command line. A filename or '-' is missing after --

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Unrecognized string Error

Hi Nayla, the error message concerns your command line. A filename or '-' is missing after --

3/7/21

Peter Pellitier, Torbjørn Rognes3

3/4/21

why not 100% matching query sequences

Torbjørn, Thank you very much for this informative response. I appreciate your replies and the

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why not 100% matching query sequences

Torbjørn, Thank you very much for this informative response. I appreciate your replies and the

3/4/21

Peter Pellitier, Torbjørn Rognes6

2/26/21

Clustering unique ASV sequences (no abundances)

Thats it. Thank you! On Wednesday, February 24, 2021 at 8:20:19 AM UTC-8 toro...@gmail.com wrote:

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Clustering unique ASV sequences (no abundances)

Thats it. Thank you! On Wednesday, February 24, 2021 at 8:20:19 AM UTC-8 toro...@gmail.com wrote:

2/26/21

Sven LE MOINE BAUER, … Frédéric Mahé10

2/19/21

Difference between vsearch and usearch clustering outputs

Sure. I ll PM you immediately. Le jeudi 18 février 2021 à 20:01:13 UTC+1, Frédéric Mahé a écrit : Hi

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Difference between vsearch and usearch clustering outputs

Sure. I ll PM you immediately. Le jeudi 18 février 2021 à 20:01:13 UTC+1, Frédéric Mahé a écrit : Hi

2/19/21

rongming liu, … Torbjørn Rognes3

2/4/21

For point mutation idenfication

Hi I need some more information on what you are actually doing to be able to help you. As Colin

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For point mutation idenfication

Hi I need some more information on what you are actually doing to be able to help you. As Colin

2/4/21

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