https://github.com/andersen-lab/ivar-bioinformatics-protocol
https://github.com/andersen-lab/ivar-bioinformatics-protocol
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/andersen-lab/ivar-bioinformatics-protocol
- Owner: andersen-lab
- Created: 2020-03-24T18:53:01.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2020-03-25T01:09:39.000Z (about 6 years ago)
- Last Synced: 2025-02-01T06:25:07.358Z (over 1 year ago)
- Size: 156 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# iVar
## bioinformatics protocol
#### This document is for the iVar package: https://github.com/andersen-lab/ivar
```Instructions for setting up the environment for running ivar```
## Software Setup
These instructions are for a 64-bit UNIX, Linux or similar envrionment.
#### Conda
iVar is installed using [Conda](https://conda.io/en/latest/)
#### Installing ivar
Install the ivar repository:
```
git clone https://github.com/andersen-lab/ivar-bioinformatics-protocol
```
Create a custom environment for ivar. Please wait while required packages are installed.
```
conda env create -f environment-ivar.yml
```
Activate the ivar environment.
```
conda activate ivar
```
After use, deactivate the environment.
```
conda deactivate
```
To remove the ivar environment use the following command.
```
conda remove --name ivar --all
```
## Commands
alignment using [bwa](https://github.com/lh3/bwa)
```
bwa index ref.fa
bwa mem ref.fa read-se.fq.gz | gzip -3 > aln-se.sam.gz
./bwa mem ref.fa read1.fq read2.fq | gzip -3 > aln-pe.sam.gz
```
ivar trim
```
ivar trim
```
ivar consensus
```
ivar filtervariants replicate-one.tsv replicate-two.tsv ... OR ivar filtervariants
```