Please use Bactopia

staphopia-ap is available from Bactopia. Please use Bactopia going forward as staphopia-ap is not longer supported.

Staphopia Analysis Pipeline

Staphopia's analysis pipeline is a set of open source tools wrapped in a Nextflow workflow. Once analysis is completed the results are stored into a database.

Installation

Currently Staphopia is setup using a Docker container.

Pull Docker Container

docker pull rpetit3/staphopia:20200127

Local Genome Analysis with staphopia.py

Staphopia pipeline, staphopia.py, processes local FASTQ files.

Usage

docker run rpetit3/staphopia:20200127 staphopia.py --help
usage: staphopia.py [-h] --fq1 FASTQ --sample SAMPLE [--fq2 FASTQ]
                    [--coverage INT] [--cpu INT] [--is_miseq] [--resume]

A wrapper for executing Staphopia Nextflow workflow.

optional arguments:
  -h, --help       show this help message and exit
  --fq1 FASTQ      Input FASTQ file.
  --sample SAMPLE  Sample name of the input.
  --fq2 FASTQ      Second FASTQ file in paired end reads.
  --coverage INT   Coverage to subsample to (Default: 100x.)
  --cpu INT        Number of processors to use.
  --is_miseq       Input is Illumina MiSeq sequencing.
  --resume         Tell nextflow to resume the run.

Example

rpetit@staphopia:~/JE2$ ls -lh
total 701M
-rw-rw-r-- 1 rpetit rpetit 360M Oct  5  2017 JE2_R1.fastq.gz
-rw-rw-r-- 1 rpetit rpetit 342M Oct  5  2017 JE2_R2.fastq.gz
rpetit@staphopia:~/JE2$ docker run --rm -v $PWD:/data rpetit3/staphopia:20200127 staphopia.py \
                                   --fq1 JE2_R1.fastq.gz --fq2 JE2_R2.fastq.gz --sample JE2 \
                                   --cpu 22 --is_miseq
rpetit@staphopia:~/JE2$ ls -lh
total 990M
drwxr-xr-x 6 rpetit rpetit 4.0K Feb 12 19:26 JE2
-rw-r--r-- 1 rpetit rpetit   45 Feb 12 19:27 JE2.md5
-rw-rw-r-- 1 rpetit rpetit 360M Feb 12 17:41 JE2_R1.fastq.gz
-rw-rw-r-- 1 rpetit rpetit 342M Feb 12 17:41 JE2_R2.fastq.gz
-rw-r--r-- 1 rpetit rpetit  38K Feb 12 19:27 JE2-staphopia.txt
-rw-r--r-- 1 rpetit rpetit 288M Feb 12 19:26 JE2.tar.gz

ENA Genome Analysis with staphopia-ena.py

Staphopia includes a modified pipeline, staphopia-ena.py, that automates the download of FASTQ files from ENA. Users give an ENA Experiment accession as the input and any corresponding FASTQs are downloaded and processed.

Usage

docker run rpetit3/staphopia:20200127 staphopia-ena.py --help
usage: staphopia-ena.py [-h] [--cpu INT] [--resume] EXPERIMENT_ACCESSION

A wrapper for executing Staphopia Nextflow workflow.

positional arguments:
  EXPERIMENT_ACCESSION  ENA experiment accession to process.

optional arguments:
  -h, --help            show this help message and exit
  --cpu INT             Number of processors to use.
  --resume              Tell nextflow to resume the run.

Example

rpetit@staphopia:~/$ mkdir SRX1114352
rpetit@staphopia:~/SRX1114352$ cd SRX1114352
rpetit@staphopia:~/SRX1114352$ docker run --rm -v $PWD:/data rpetit3/staphopia:20200127 staphopia-ena.py SRX1114352 --cpu 22
rpetit@staphopia:~/SRX1114352$ ls -lh
total 204M
-rw-r--r-- 1 root root   52 Apr 16 17:46 SRX1114352.md5
-rw-r--r-- 1 root root  39K Apr 16 17:46 SRX1114352-staphopia.txt
-rw-r--r-- 1 root root 204M Apr 16 17:46 SRX1114352.tar.gz

List of Tools

Below is a list of the software programs used in Staphopia's pipeline. We would like to thank the authors of these tools!

Tool	Version
Ariba	2.10.2
assembly-summary	0.1
BBDuk	37.66
bedtools	2.26
BLAST+	2.7.1
BWA	0.7.17
ena-dl	0.1
GATK	3.8
illumina-cleanup	0.3
Jellyfish	2.2.6
MentaLiST	0.1.3
Nextflow	0.28.2
Picard	2.14.1
PROKKA	1.12
Samtools	1.6
SPAdes	3.11.1
vcf-annotator	0.4

Contact

Robert Petit [email protected]