# Nextalign + Snakemake

**URL:** <https://nextstrain.discourse.group/t/nextalign-snakemake/352>\
**Category:** Uncategorized\
**Created:** [February 18, 2021, 1:37pm UTC](https://nextstrain.discourse.group/t/nextalign-snakemake/352 "2021-02-18T13:37:55Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![andersonbrito](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/andersonbrito/32/72_2.png) [@andersonbrito](https://nextstrain.discourse.group/u/andersonbrito)\
**Post date:** [February 18, 2021, 1:37pm UTC](https://nextstrain.discourse.group/t/nextalign-snakemake/352/1 "2021-02-18T13:37:56Z")

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Hi all,

I had a go on Nextalign in my local machine yesterday, great tool. Getting alignments as codon and protein alignments is a plus.

As Nextalign may not yet be available within augur, I was wondering what would be the best way to add it in a environment, so it can be run as a component of a Snakemake workflow.

Any suggestions?

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**Author:** ![rneher](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/rneher/32/20_2.png) [@rneher](https://nextstrain.discourse.group/u/rneher)\
**Post date:** [February 19, 2021, 8:37am UTC](https://nextstrain.discourse.group/t/nextalign-snakemake/352/2 "2021-02-19T08:37:35Z")

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Hi Anderson,

you can simply download a binary. See “Downloads” section on

> **[Nextclade](https://clades.nextstrain.org/)**
>
> Clade assignment, mutation calling, and sequence quality checks

There are branches of `ncov` that use nextalign. Will hopefully be opt-in on master soon.

This one is built on current (new) master but doesn’t have the protein alignments yet:

> **[nextstrain/ncov](https://github.com/nextstrain/ncov/tree/nextalign-rebased)**
>
> nextalign-rebased

This one is diverged and served more as a playground but has the protein alignments:

> **[nextstrain/ncov](https://github.com/nextstrain/ncov/tree/nextalign)**
>
> nextalign

let us know if you run into issues,

richard

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<div class="post-metadata">

**Author:** ![andersonbrito](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/andersonbrito/32/72_2.png) [@andersonbrito](https://nextstrain.discourse.group/u/andersonbrito)\
**Post date:** [February 19, 2021, 1:56pm UTC](https://nextstrain.discourse.group/t/nextalign-snakemake/352/3 "2021-02-19T13:56:20Z")

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Thank you, @rneher. Good call. I’ll just add the binary inside a scripts folder, and that should work just fine, indeed.

I’ll let you know if I run into any issues.  
Best

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**Author:** ![trs](https://yyz1.discourse-cdn.com/flex031/user_avatar/nextstrain.discourse.group/trs/32/5_2.png) [@trs](https://nextstrain.discourse.group/u/trs)\
**Post date:** [February 23, 2021, 5:59pm UTC](https://nextstrain.discourse.group/t/nextalign-snakemake/352/4 "2021-02-23T17:59:50Z")

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Following up for future readers to add that `nextalign` is also included in the [`nextstrain/base` Docker image](https://github.com/nextstrain/docker-base), for anyone using a containerized workflow (with or without the Nextstrain CLI).