# Classify Contigs to reference sequences

**URL:** <https://help.galaxyproject.org/t/classify-contigs-to-reference-sequences/15880>\
**Category:** usegalaxy.org support\
**Created:** [July 2, 2025, 9:02pm UTC](https://help.galaxyproject.org/t/classify-contigs-to-reference-sequences/15880 "2025-07-02T21:02:39Z")\
**Posts on this page:** 1\
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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [July 14, 2025, 7:02pm UTC](https://help.galaxyproject.org/t/classify-contigs-to-reference-sequences/15880/4 "2025-07-14T19:02:44Z")

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Thanks @Jon_Colman for reminding me. Let’s group all of your discussions together here.

- [Bowtie2 Mapping Issues](https://help.galaxyproject.org/t/bowtie2-mapping-issues/15333)
- [FASTQ Mapping to Reference Issues](https://help.galaxyproject.org/t/fastq-mapping-to-reference-issues/15216)

I know those weren’t really resolved yet but I think the prior advice from Peter is good (he also works in public health). Your question is about the scientific analysis strategy, and the “standardized” bioinformatics methods I can help with here will not be enough. Your analysis will require in depth detective work – the baseline alignment generation is just the very first step! I think you will need find someone private to collaborate with.

We can leave this one open to attract potential partners, but casting a wider net is almost certainly needed. Academic or hospital labs working in infectious disease areas are probably your best options. I know this isn’t helpful but I do hope this works out.

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