Requirements:
Python 2.7.* https://www.python.org/downloads/
Miniconda https://conda.io/miniconda.html
## 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]wget -c metamed.rwebox.com/data/bowtie2index.tar.gzor: Download Here
usage: metapipe.py [-h] {WGS,16S} ...
WGS Input whole genome sequencing data
16S Input 16s rDNA sequencing data 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. |
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] |
#SampleID BarcodeSequence LinkerPrimerSequence Description
SRR048044 TCAGCGCAAC CCGTCAATTCMTTTRAGT female_Stool
| #BGC names | #Read count |
|---|---|
| Epilancin 15X biosynthetic gene cluster | 19 |
| Salivaricin 9 biosynthetic gene cluster | 4 |
| #BGC names | #Percentage score |
|---|---|
| Alpha-galactosylceramide biosynthetic gene cluster | 0.3933 |
| Flavecin biosynthetic gene cluster | 0.0139 |