# Handling Paired-End Reads in ShortBRED

**URL:** <https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878>\
**Category:** ShortBRED\
**Created:** [December 8, 2021, 2:09pm UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878 "2021-12-08T14:09:15Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![plicht](https://avatars.discourse-cdn.com/v4/letter/p/e95f7d/32.png) [@plicht](https://forum.biobakery.org/u/plicht)\
**Post date:** [December 8, 2021, 2:09pm UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878/1 "2021-12-08T14:09:15Z")

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Dear biobakery-Team,

I want to process paired-end reads with ShortBRED. To my knowledge, specifying 2 reads is not mentioned in the user manual. However, ShortBRED runs with 2 parsed reads and it was [discussed in this thread](https://forum.biobakery.org/t/specifying-strands-in-usearch-within-shortbred-quantify/2659) as well.

How does ShortBRED subsequently calculate hits? Will it be twice as much hits as compared to single-end reads?

Best  
Philipp

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**Author:** ![adler-sudo](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/adler-sudo/32/1146_2.png) [@adler-sudo](https://forum.biobakery.org/u/adler-sudo)\
**Post date:** [December 10, 2021, 2:47am UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878/2 "2021-12-10T02:47:57Z")

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I’m hoping for additional clarification on paired-end reads, too. How is shortBRED accounting for the pairs when determining reads aligning to marker sequences?

It seems that you would want to assemble your paired-end reads into contigs and then pass these contigs into shortBRED, but based on the thread plicht references and based on information I’ve found elsewhere, it sounds like biobakery team recommends just passing R1 and R2 in at the same time.

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**Author:** ![plicht](https://avatars.discourse-cdn.com/v4/letter/p/e95f7d/32.png) [@plicht](https://forum.biobakery.org/u/plicht)\
**Post date:** [January 4, 2022, 2:04pm UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878/3 "2022-01-04T14:04:12Z")

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Any suggestions/ideas here?

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**Author:** ![bmtalbot](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/bmtalbot/32/582_2.png) [@bmtalbot](https://forum.biobakery.org/u/bmtalbot)\
**Post date:** [February 8, 2022, 4:37pm UTC](https://forum.biobakery.org/t/handling-paired-end-reads-in-shortbred/2878/4 "2022-02-08T16:37:25Z")

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Hi all,  
I wanted to revitalize this topic as this is something I am curious about as well. How should someone interpret the output of two paired-end reads run together? Would it be a different outcome than if the paired-end reads were assembled?  
Thank you for your input!  
Brooke