README.md 1.12 KB
Newer Older
peguerin's avatar
peguerin committed
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
bash_vsearch_ecotag 
===================

# Table of contents

1. [Introduction](#1-introduction)
2. [Installation](#2-installation)
	1. [Requirements](#21-requirements)
	2. [Initialisation](#22-initialisation)
3. [Reporting bugs](#3-reporting-bugs)
4. [Running the pipeline](#4-running-the-pipeline)

-----------------

# 1. Introduction

Pipeline for edna paired end data to do :
* Assembly, demultiplexing, dereplicate with vsearch/cutadapt
* taxonomy assignation with ECOTAG


peguerin's avatar
scripts    
peguerin committed
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
To download the project
```
git clone https://gitlab.mbb.univ-montp2.fr/edna/bash_vsearch_ecotag.git
```

To run the whole pipeline into a single command
```
NCORES=16
nohup bash main.sh path/to/fastqdat path/to/refdatabase $NCORES &
```

* path/to/fastqdat : absolute path to a folder with fastq files and .dat information
* path/to/refdatabase : absolute path to the folder of reference database
* $NCORES : number of available cores for this job

Example of command
```
PATH_FASTQC="/media/superdisk/edna/donnees/rhone_test/"
PATH_REFDAT="/media/superdisk/edna/donnees/reference_database_teleo/"
NCORES=16
nohup bash main.sh $PATH_FASTQC $PATH_REFDAT $NCORES &
```