<commit_before>---
layout: post
title: "README for the SILVA v119 reference files"
author: "<NAME>"
date: "August 8, 2014"
comments: true
---
The good people at [SILVA](http://arb-silva.de) have released a new version of the SILVA database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the [mothur-compatible reference files](http://www.mothur.org/wiki/Silva_reference_files).

##Curation of references
###Getting the data in and out of the ARB database
This README file explains how we generated the silva reference files for use with mothur's classify.seqs and align.seqs commands. I'll assume that you have a functioning copy of arb installed on your comptuer. For this README we are using version 6.0. First we need to download the database and decompress it. From the command line we do the following:


{% highlight bash %}
wget -N http://www.arb-silva.de/fileadmin/arb_web_db/release_119/ARB_files/SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz
tar xvzf *arb.tgz
arb SSURef_NR99_119_SILVA_14_07_14_opt.arb
{% endhighlight %}

This will launch us into the arb environment with the ''Ref NR 99'' database opened. This database has 534,968 sequences within it that are not more than 99% similar to each other. The release notes for [this database](http://www.arb-silva.de/documentation/release-119/) as well as the idea behind the [non-redundant database](http://www.arb-silva.de/projects/ssu-ref-nr/) are available from the silva website. Within arb do the following:  

1. Click the search button<commit_msg>Fixed typo in my name<commit_after>---
layout: post
title: "README for the SILVA v119 reference files"
author: "<NAME>"
date: "August 8, 2014"
comments: true
---
The good people at [SILVA](http://arb-silva.de) have released a new version of the SILVA database. A little bit of tweaking is needed to get their files to be compatible with mothur. This README document describes the process that I used to generate the [mothur-compatible reference files](http://www.mothur.org/wiki/Silva_reference_files).

##Curation of references
###Getting the data in and out of the ARB database
This README file explains how we generated the silva reference files for use with mothur's classify.seqs and align.seqs commands. I'll assume that you have a functioning copy of arb installed on your comptuer. For this README we are using version 6.0. First we need to download the database and decompress it. From the command line we do the following:


{% highlight bash %}
wget -N http://www.arb-silva.de/fileadmin/arb_web_db/release_119/ARB_files/SSURef_NR99_119_SILVA_14_07_14_opt.arb.tgz
tar xvzf *arb.tgz
arb SSURef_NR99_119_SILVA_14_07_14_opt.arb
{% endhighlight %}

This will launch us into the arb environment with the ''Ref NR 99'' database opened. This database has 534,968 sequences within it that are not more than 99% similar to each other. The release notes for [this database](http://www.arb-silva.de/documentation/release-119/) as well as the idea behind the [non-redundant database](http://www.arb-silva.de/projects/ssu-ref-nr/) are available from the silva website. Within arb do the following:  

1. Click the search button
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