---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: Sequence Subsetting - Pgenerosa_v70 Genome Assembly with faidx
date: '2019-02-11 20:41'
tags:
  - faix
  - Panopea generosa
  - geoduck
  - Pgenerosa_v70
categories:
  - 2019
  - Miscellaneous
---
[Steven asked to subset geoduck assembly](https://github.com/RobertsLab/resources/issues/572) in to >10kbp and >30kbp groups. Here are the commands, using [```faidx```](https://github.com/mdshw5/pyfaidx):


#### >10kbp subsetting
```
faidx --size-range 10000,1000000000 Pgenerosa_v070.fa > Pgenerosa_v071.fasta
```

#### Index new FastA
```
faidx Pgenerosa_v071.fasta
```
---

#### >30kbp subsetting
```
faidx --size-range 30000,1000000000 Pgenerosa_v070.fa > Pgenerosa_v073.fasta

```
#### Index new FastA
```
faidx Pgenerosa_v073.fasta
```
---

#### MD5 checksums
35b6b653b543ebb7f3631e68523ab595  Pgenerosa_v071.fasta
ce81a0fc127e6cc0cbf216eb85b87749  Pgenerosa_v073.fasta

---

All files were copied to our [genomic databank](http://owl.fish.washington.edu/halfshell/genomic-databank/) on Owl.

See our [Genomic Resources wiki (GitHub)](https://github.com/RobertsLab/resources/wiki/Genomic-Resources) for a more concise overview.