# \#chimera **URL:** https://forum.qiime2.org/tag/chimera/32.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [QIIME2 non-chimeric reads](https://forum.qiime2.org/t/qiime2-non-chimeric-reads/33770)
**Author:** [@jlco](https://forum.qiime2.org/u/jlco)\ **Replies:** 3\ **Last updated:** [November 10, 2025, 3:09pm UTC](https://forum.qiime2.org/t/qiime2-non-chimeric-reads/33770 "2025-11-10T15:09:26Z")
Hi Supporting Team. I got a problem with regards to the dada2 output on non-chimeric reads during a dry run. Here is the output file regarding the dada2 result. dental-test-dada2-stats.qzv (1.2 MB) Observe that the non… --- ## [Chimeras - dada2 settings, and optimal PCR polymerase?](https://forum.qiime2.org/t/chimeras-dada2-settings-and-optimal-pcr-polymerase/33717)
**Author:** [@Mikael\_Niku](https://forum.qiime2.org/u/Mikael_Niku)\ **Replies:** 1\ **Last updated:** [October 13, 2025, 2:19pm UTC](https://forum.qiime2.org/t/chimeras-dada2-settings-and-optimal-pcr-polymerase/33717 "2025-10-13T14:19:11Z")
Please read the following before posting! Is this post about a User Support Question? Those include questions about specific results while running QIIME 2, warnings observed while running a QIIME 2 command. Please do not… --- ## [Chimera removal dilemma in 16S V3–V4: necessary when using Kraken2/Bracken?](https://forum.qiime2.org/t/chimera-removal-dilemma-in-16s-v3-v4-necessary-when-using-kraken2-bracken/33679)
**Author:** [@christopherwilliamle](https://forum.qiime2.org/u/christopherwilliamle)\ **Replies:** 8\ **Last updated:** [September 26, 2025, 10:22pm UTC](https://forum.qiime2.org/t/chimera-removal-dilemma-in-16s-v3-v4-necessary-when-using-kraken2-bracken/33679 "2025-09-26T22:22:06Z")
Hi everyone, I would like to know how you usually deal with chimeras in 16S data, given that Kraken2 does not explicitly remove them (and, as far as I understand, it might actually handle them relatively well). Here’s … --- ## [Effect of primer removal on chimera detection in DADA2](https://forum.qiime2.org/t/effect-of-primer-removal-on-chimera-detection-in-dada2/33605)
**Author:** [@Shreya](https://forum.qiime2.org/u/Shreya)\ **Replies:** 8\ **Last updated:** [August 25, 2025, 6:14pm UTC](https://forum.qiime2.org/t/effect-of-primer-removal-on-chimera-detection-in-dada2/33605 "2025-08-25T18:14:37Z")
Hello QIIME2 community, I am working on gut microbiome analysis using QIIME2 and facing challenges with high levels of chimeras in my dataset. After going through the literature, I found several reports suggesting that … --- ## [Low percentage of non-quimeric reads after dada2](https://forum.qiime2.org/t/low-percentage-of-non-quimeric-reads-after-dada2/33129)
**Author:** [@amonm82](https://forum.qiime2.org/u/amonm82)\ **Replies:** 3\ **Last updated:** [May 14, 2025, 4:02pm UTC](https://forum.qiime2.org/t/low-percentage-of-non-quimeric-reads-after-dada2/33129 "2025-05-14T16:02:10Z")
Hi everyone, I sent my samples for 16S rRNA amplicon sequencing (targeting the V4–V5 region) in two separate batches. The sequencing company provided the raw demultiplexed data, with primers and barcodes already remove… --- ## [DADA2 denoise is removing more than 50% of the data](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569)
**Author:** [@ankurnaqib](https://forum.qiime2.org/u/ankurnaqib)\ **Replies:** 4\ **Last updated:** [March 10, 2023, 4:19pm UTC](https://forum.qiime2.org/t/dada2-denoise-is-removing-more-than-50-of-the-data/25569 "2023-03-10T16:19:06Z")
Hi, I am going through the usual QIIME2 pipeline and I noticed that DADA2 denoise is removing almost 50% of the data (as seen in the denoising\_stats.qzv file). denoising\_stats.qzv (1.2 MB) I tried running the same dat… --- ## [Error with dada2 (return code 1) isBimeraDenovoTable](https://forum.qiime2.org/t/error-with-dada2-return-code-1-isbimeradenovotable/21308)
**Author:** [@mikatsume](https://forum.qiime2.org/u/mikatsume)\ **Replies:** 7\ **Last updated:** [November 17, 2021, 5:44pm UTC](https://forum.qiime2.org/t/error-with-dada2-return-code-1-isbimeradenovotable/21308 "2021-11-17T17:44:54Z")
Hi, this is my first time using qiime, the thing is the sequences that were given to me were paired-end fastq files (demultiplexed) so i followed the casava import tutorial. then i tried to run dada2 to denoise: qiim… --- ## [running uchime-ref after deblur -- general questions and parameters](https://forum.qiime2.org/t/running-uchime-ref-after-deblur-general-questions-and-parameters/20504)
**Author:** [@anna-schrecengost](https://forum.qiime2.org/u/anna-schrecengost)\ **Replies:** 9\ **Last updated:** [September 13, 2021, 6:13pm UTC](https://forum.qiime2.org/t/running-uchime-ref-after-deblur-general-questions-and-parameters/20504 "2021-09-13T18:13:09Z")
Hi, I want to try using qiime vsearch uchime-ref on my ASVs that I've obtained after running Deblur. This is because I've noticed there are still a lot of chimeras in my dataset. On a side note -- has anyone else had thi… --- ## [Used degenerate primers for sequencing, concerned that my reads are being confused as chimeras](https://forum.qiime2.org/t/used-degenerate-primers-for-sequencing-concerned-that-my-reads-are-being-confused-as-chimeras/20578)
**Author:** [@bkramer](https://forum.qiime2.org/u/bkramer)\ **Replies:** 1\ **Last updated:** [September 1, 2021, 9:49pm UTC](https://forum.qiime2.org/t/used-degenerate-primers-for-sequencing-concerned-that-my-reads-are-being-confused-as-chimeras/20578 "2021-09-01T21:49:37Z")
Hello, I have demultiplexed paired-end reads that were amplified with the igk3/dvv primer pair, which has been used to taxonomically classify diazotrophic communities. These primers: IGK = GCNWTHTAYGGNAARGGNGGNATHGGNAA … --- ## [DADA2：low non-chimeric](https://forum.qiime2.org/t/dada2-low-non-chimeric/20594)
**Author:** [@Susun](https://forum.qiime2.org/u/Susun)\ **Replies:** 1\ **Last updated:** [August 31, 2021, 2:09pm UTC](https://forum.qiime2.org/t/dada2-low-non-chimeric/20594 "2021-08-31T14:09:40Z")
Dear all: When I use DADA2 to process my data with qiime2-2021.4 , I got very low non-chimerism. My sequencing platform is Novaseq. This is demux picture. The command I use istime qiime dada2 denoise-paired \\ --i-… --- ## [What are the criteria for choosing the optimal "--p-min-fold-parent-over-abundance" parameter in dada2?](https://forum.qiime2.org/t/what-are-the-criteria-for-choosing-the-optimal-p-min-fold-parent-over-abundance-parameter-in-dada2/20124)
**Author:** [@nikopech](https://forum.qiime2.org/u/nikopech)\ **Replies:** 1\ **Last updated:** [July 9, 2021, 9:55pm UTC](https://forum.qiime2.org/t/what-are-the-criteria-for-choosing-the-optimal-p-min-fold-parent-over-abundance-parameter-in-dada2/20124 "2021-07-09T21:55:13Z")
Hello everyone, I am currently trying to analyze data from 16S amplicon sequencing (Nextera XT chemistry for Illumina), and during sequence processing with DADA2, I am getting only a small percentage (~ 50%) of nonchime… --- ## [high chimera rate in dada2](https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935)
**Author:** [@Claire010](https://forum.qiime2.org/u/Claire010)\ **Replies:** 3\ **Last updated:** [October 17, 2020, 6:08am UTC](https://forum.qiime2.org/t/high-chimera-rate-in-dada2/16935 "2020-10-17T06:08:47Z")
Hi Bod @Mehrbod\_Estaki, Thanks a lot for the explanation about Denoising. Following this section, actually I have a question about chimera. In my dataset using DADA2 for denoising, over 90% of the merged ASVs are infer… --- ## [Do I need to remove chimera with qiime vsearch uchime-denovo after denosing by Dada2](https://forum.qiime2.org/t/do-i-need-to-remove-chimera-with-qiime-vsearch-uchime-denovo-after-denosing-by-dada2/15305)
**Author:** [@Tintin](https://forum.qiime2.org/u/Tintin)\ **Replies:** 6\ **Last updated:** [June 13, 2020, 3:25pm UTC](https://forum.qiime2.org/t/do-i-need-to-remove-chimera-with-qiime-vsearch-uchime-denovo-after-denosing-by-dada2/15305 "2020-06-13T15:25:51Z")
Hello everybody, I have used Dada2 for the denoising step. As I know Dada2 also includes removing chimera. I am wondering that it is necessary to remove chimera with qiime vsearch uchime-denovo after denosing by Dada2 … --- ## [Losing reads as chimeras](https://forum.qiime2.org/t/losing-reads-as-chimeras/14629)
**Author:** [@hsapers](https://forum.qiime2.org/u/hsapers)\ **Replies:** 10\ **Last updated:** [May 18, 2020, 6:56pm UTC](https://forum.qiime2.org/t/losing-reads-as-chimeras/14629 "2020-05-18T18:56:08Z")
Hello Thank you for all the help and support in this forum! I seem to be losing a lot of reads during denoising. I've checked a couple of posts that have suggested only using fwd reads, making sure primers are removed, … --- ## [DADA2 Denoise: Different Chimera parameters same output](https://forum.qiime2.org/t/dada2-denoise-different-chimera-parameters-same-output/14394)
**Author:** [@Carlmed00](https://forum.qiime2.org/u/Carlmed00)\ **Replies:** 12\ **Last updated:** [April 20, 2020, 5:26pm UTC](https://forum.qiime2.org/t/dada2-denoise-different-chimera-parameters-same-output/14394 "2020-04-20T17:26:05Z")
My query isn't really an error but I attempted to run my demux file for denoise qiime dada2 denoise-paired --i-demultiplexed-seqs RBD\_AB\_MBRS\_demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 200 -… --- ## [Statistics from de novo chimera removal](https://forum.qiime2.org/t/statistics-from-de-novo-chimera-removal/14389)
**Author:** [@afrinaad](https://forum.qiime2.org/u/afrinaad)\ **Replies:** 5\ **Last updated:** [April 10, 2020, 2:39pm UTC](https://forum.qiime2.org/t/statistics-from-de-novo-chimera-removal/14389 "2020-04-10T14:39:11Z")
Hi everyone, I am currently trying to do comparison between DADA2 and the OTU clustering methods. As we know, chimera removal is already included in DADA2 while for OTU clustering method, we will have to do it 'manually… --- ## [Up to 97% of sequences being removed by filtering/denoising in DADA2](https://forum.qiime2.org/t/up-to-97-of-sequences-being-removed-by-filtering-denoising-in-dada2/12943)
**Author:** [@nutrishinn](https://forum.qiime2.org/u/nutrishinn)\ **Replies:** 4\ **Last updated:** [December 20, 2019, 9:45pm UTC](https://forum.qiime2.org/t/up-to-97-of-sequences-being-removed-by-filtering-denoising-in-dada2/12943 "2019-12-20T21:45:49Z")
I ran QIIME2 2018.4 and 2018.6 in September 2018 on MiSeq single-end sequencing data and realized that a large number of my sequences were being cut out after using DADA2, with one sample being cut down from ~3500 to 631… --- ## [DADA2 denoise-single chimera removal inconsistence](https://forum.qiime2.org/t/dada2-denoise-single-chimera-removal-inconsistence/10342)
**Author:** [@Cotton](https://forum.qiime2.org/u/Cotton)\ **Replies:** 16\ **Last updated:** [August 2, 2019, 6:52am UTC](https://forum.qiime2.org/t/dada2-denoise-single-chimera-removal-inconsistence/10342 "2019-08-02T06:52:17Z")
Hi to all! I'm running QIIME2 2019.1 which is installed by anaconda on a CentOS7 server. I meet a very weird problem. I have some single-end demultiplexed 16S amplicon sequencing data. Then I imported the data twice by… --- ## [fasta file analysis in QIIME2](https://forum.qiime2.org/t/fasta-file-analysis-in-qiime2/9601)
**Author:** [@Brandon](https://forum.qiime2.org/u/Brandon)\ **Replies:** 9\ **Last updated:** [May 10, 2019, 5:51pm UTC](https://forum.qiime2.org/t/fasta-file-analysis-in-qiime2/9601 "2019-05-10T17:51:56Z")
Hi, developer, Appreciate your time. I have multiple fasta files, each fasta is one sample. I want to pick OTU/ASV and check chimeras in QIIME2. May I know the procedure? Sincerely. Brandon --- ## [Too many chimeras in my samples?](https://forum.qiime2.org/t/too-many-chimeras-in-my-samples/9015)
**Author:** [@MiniMicrobe](https://forum.qiime2.org/u/MiniMicrobe)\ **Replies:** 2\ **Last updated:** [April 15, 2019, 4:12pm UTC](https://forum.qiime2.org/t/too-many-chimeras-in-my-samples/9015 "2019-04-15T16:12:52Z")
Hi all I have been looking at the first sequencing run of my data which comes from chronic wound infection swabs. The data is Illumina 2x300 paired end reads and samples were prepared following the human microbiome pro… --- ## [Chimera check in dada2 and with vsearch uchime-denovo](https://forum.qiime2.org/t/chimera-check-in-dada2-and-with-vsearch-uchime-denovo/4306)
**Author:** [@alfanon](https://forum.qiime2.org/u/alfanon)\ **Replies:** 3\ **Last updated:** [May 28, 2018, 2:41pm UTC](https://forum.qiime2.org/t/chimera-check-in-dada2-and-with-vsearch-uchime-denovo/4306 "2018-05-28T14:41:21Z")
Dear all, I tried dada2 on my data. After that I tried also vsearch uchime-denovo as suggested in the tutorial Identifying and filtering chimeric feature sequences with q2-vsearch — QIIME 2 2018.4.0 documentation. I als… --- ## [Plugin error: when doing the de novo chimera checking](https://forum.qiime2.org/t/plugin-error-when-doing-the-de-novo-chimera-checking/3125)
**Author:** [@mly](https://forum.qiime2.org/u/mly)\ **Replies:** 4\ **Last updated:** [February 22, 2018, 7:42pm UTC](https://forum.qiime2.org/t/plugin-error-when-doing-the-de-novo-chimera-checking/3125 "2018-02-22T19:42:07Z")
Hi ~~, i was following Identifying and filtering chimeric feature sequences with q2-vsearch — QIIME 2 2018.2.0 documentation for de novo chimera checking. it says there is plugin error. "Plugin error from vsearch: Comm… --- ## [Chimera check questions](https://forum.qiime2.org/t/chimera-check-questions/2409)
**Author:** [@steff1088](https://forum.qiime2.org/u/steff1088)\ **Replies:** 9\ **Last updated:** [January 5, 2018, 9:15pm UTC](https://forum.qiime2.org/t/chimera-check-questions/2409 "2018-01-05T21:15:21Z")
Hi everybody, Release 12 enables chimera checking with uchime-ref or uchime-denovo. What method is the more accurate one with higher efficacy of chimeric sequence removal? Also, my workflow is Dereplication Open-refer… --- ## [Chimera separate filtering](https://forum.qiime2.org/t/chimera-separate-filtering/2076)
**Author:** [@steff1088](https://forum.qiime2.org/u/steff1088)\ **Replies:** 2\ **Last updated:** [December 22, 2017, 5:57pm UTC](https://forum.qiime2.org/t/chimera-separate-filtering/2076 "2017-12-22T17:57:58Z")
Hi! I was looking for an option to check for chimeras in q2. For various reasons I can't use DADA2 and Deblur, and my data do not carry quality information. Thank you!! -steffen --- ## [Estimated time for DADA2 process](https://forum.qiime2.org/t/estimated-time-for-dada2-process/941)
**Author:** [@yeojuny](https://forum.qiime2.org/u/yeojuny)\ **Replies:** 8\ **Last updated:** [December 22, 2017, 5:33pm UTC](https://forum.qiime2.org/t/estimated-time-for-dada2-process/941 "2017-12-22T17:33:45Z")
Hi, I'm running DADA2 in qiime2 now, V3-V4 Paired-end, total over 1500 samples, around 50G size of sequence files (Foward+Reverse). I started almost two weeks ago but it's still running, and I don't know when it will … --- ## [Identifying and filtering chimeric feature sequences with vsearch](https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252)
**Author:** [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Replies:** 0\ **Last updated:** [December 17, 2017, 2:22pm UTC](https://forum.qiime2.org/t/identifying-and-filtering-chimeric-feature-sequences-with-vsearch/2252 "2017-12-17T14:22:05Z")
This community tutorial has been migrated to our official documentation. Please refer to that tutorial instead. ▶ Click to see original community tutorial --- ## [Problem with DADA2](https://forum.qiime2.org/t/problem-with-dada2/1329)
**Author:** [@djcabral92](https://forum.qiime2.org/u/djcabral92)\ **Replies:** 2\ **Last updated:** [October 2, 2017, 8:47pm UTC](https://forum.qiime2.org/t/problem-with-dada2/1329 "2017-10-02T20:47:13Z")
Hello, I am trying to use the dada2 denoise-paired command on version 2017.8 but I keep experiencing the same error. The code I'm using is: qiime dada2 denoise-paired \\ --i-demultiplexed-seqs ~/data/djcabral/qiime2\_… --- ## [Chimera checking and bar plots](https://forum.qiime2.org/t/chimera-checking-and-bar-plots/785)
**Author:** [@eDNA](https://forum.qiime2.org/u/eDNA)\ **Replies:** 3\ **Last updated:** [July 10, 2017, 9:53pm UTC](https://forum.qiime2.org/t/chimera-checking-and-bar-plots/785 "2017-07-10T21:53:33Z")
Hello, I used another software to obtain a feature table and representative sequences because I cannot use Qiime 2 to process my sequence data. I have successfully imported the feature table and representative sequences…