README

Metapipe: Preprocessing pipeline for MetaMed website

Download and Install:

Requirements:
Python 2.7.* https://www.python.org/downloads/
Miniconda https://conda.io/miniconda.html

Linux or Macox command line installation

## First, install the environment
bash install.sh
## Second, activate the environment before run this pipeline
source activate metapipe
## Finally, run metapipe
python metapipe.py [options]

Download bowtie2 index (for WGS/shotgun data)

wget -c metamed.rwebox.com/data/bowtie2index.tar.gz

or: Download Here

Main arguments:

usage: metapipe.py [-h] {WGS,16S} ... 
    WGS       Input whole genome sequencing data 
    16S       Input 16s rDNA sequencing data 

WGS Mode

usage: metapipe.py WGS [-h] --input INPUT --outdir OUTDIR --outprefix
                       OUTPREFIX [--keeptemp] --index INDEX [--thread THREAD]
                       [--sensitive]

Example:

python metapipe.py WGS --input wgs_r1.fastq,wgs_r2.fastq --index ./bowtie2index/mibig_bgc --outdir ./wgs_result 
--outprefix wgs_test --thread 4 --sensitive

Parameter	Introduction
-h, --help	show this help message and exit
--input INPUT	Input fastq files ("a.fq" for sinle end data and "s1.fq,s2.fq" for pair end data )
--outdir OUTDIR	Output directory [deafult:./]
--outprefix OUTPREFIX	Output filename prefix [default:output]
--keeptemp	Keep all temp files for mapping and expression estimation
--index INDEX	Bowtie2 index prefix
--thread THREAD	Number of cpu cores used for this pipeline [default:1]
--sensitive	Turn this options on if BGC mapping rate is very low in normal mode.

16S rDNA Mode

usage: metapipe.py 16S [-h] --input INPUT --outdir OUTDIR --outprefix
                       OUTPREFIX [--keeptemp] --mapfile MAPFILE
                       [--filter FILTER]

Example:

python metapipe.py 16S --input ./16s.fastq --outdir ./16s_result --outprefix 16s_test --mapfile ./16s_map.txt

Parameter	Introduction
-h, --help	show this help message and exit
--input INPUT	Input fastq files
--outdir OUTDIR	Output directory [deafult:./]
--outprefix OUTPREFIX	Output filename prefix [default:output]
--keeptemp	Keep all temp files for mapping and expression estimation
--mapfile MAPFILE	Sequencing barcode file in qiime format
--filter FILTER	Filter out microbes lower than the ratio of metagenome [default:0.01]

Sequencing barcode file in qiime format(mapfile) example in tab-delimited format

#SampleID BarcodeSequence LinkerPrimerSequence Description
SRR048044 TCAGCGCAAC CCGTCAATTCMTTTRAGT female_Stool

Example output file

WGS mode output

#BGC names	#Read count
Epilancin 15X biosynthetic gene cluster	19
Salivaricin 9 biosynthetic gene cluster	4

16S rDNA mode output

#BGC names	#Percentage score
Alpha-galactosylceramide biosynthetic gene cluster	0.3933
Flavecin biosynthetic gene cluster	0.0139