# Dual indexing options?

**URL:** https://forum.qiime2.org/t/dual-indexing-options/8987
**Category:** User Support
**Created:** [March 26, 2019, 7:06pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987 "2019-03-26T19:06:39Z")
**Posts on this page:** 5
**Page:** 1

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### Author: ![Steph\_Hp](https://forum.qiime2.org/user_avatar/forum.qiime2.org/steph_hp/32/4147_2.png) [@Steph\_Hp](https://forum.qiime2.org/u/Steph_Hp)
#### Post date: [March 26, 2019, 7:06pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987/1 "2019-03-26T19:06:39Z")

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Hey! I konw this question is too old but I'd like to know if there is an option avaialable these days for this "dual-indexing " in the demultiplexing

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [March 26, 2019, 7:39pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987/2 "2019-03-26T19:39:55Z")

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Qiime 2 does not support dual-index reads, according to [the documentation](https://docs.qiime2.org/2019.1/tutorials/qiime2-for-experienced-microbiome-researchers/?highlight=dual#demultiplexing-sequences). 😢

But it does suggest another option!

> So for the time being, this type of demultiplexing needs to be done outside of QIIME 2 using other tools, for example [bcl2fastq](https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html).

Let me know if that works for you.

Colin  
P.S. Github issue [cross ref](https://github.com/qiime2/q2-demux/issues/55) for #55 q2-demux

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### Author: ![Steph\_Hp](https://forum.qiime2.org/user_avatar/forum.qiime2.org/steph_hp/32/4147_2.png) [@Steph\_Hp](https://forum.qiime2.org/u/Steph_Hp)
#### Post date: [March 27, 2019, 3:51pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987/3 "2019-03-27T15:51:35Z")

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In order to continue with the topic in the forum.. Colin... you say... it is allowed to do the dual demultiplexing in QIIME 1 and then continue with QIIME 2 ????

Thanks!

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### Author: ![colinbrislawn](https://forum.qiime2.org/user_avatar/forum.qiime2.org/colinbrislawn/32/6221_2.png) [@colinbrislawn](https://forum.qiime2.org/u/colinbrislawn)
#### Post date: [March 27, 2019, 4:37pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987/4 "2019-03-27T16:37:32Z")

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Yes, yes you could!

After demultiplexing and quality filtering with Qiime 1, you will have a `seqs.fna` file with qiime labels. You can them import that `seqs.fna` file into a Qiime 2 `seqs.qza` artifact.  
[https://docs.qiime2.org/2019.1/tutorials/importing/#sequences-without-quality-information-i-e-fasta](https://docs.qiime2.org/2019.1/tutorials/importing/#sequences-without-quality-information-i-e-fasta)

Let me know if this method works for you!

Colin

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### Author: ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 27, 2019, 10:37pm UTC](https://forum.qiime2.org/t/dual-indexing-options/8987/5 "2019-04-27T22:37:34Z")

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