NGS, ribosomal, rRNA, snakemake, sequana
Project description
This is is the ribofinder pipeline from the Sequana project
- Overview:
Simple parallele workflow to detect and report ribosomal content
- Input:
FastQ files
- Output:
HTML reports
- Status:
production
- Citation:
Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
Installation
You must install Sequana first (use –upgrade to get the latest version installed):
pip install sequana --upgrade
Then, just install this package:
pip install sequana_ribofinder --upgrade
Usage
This pipeline scans input fastq.gz files found in the local directory and identify the proportion of ribosomal content.
For help, please type:
sequana_ribofinder --help
The following command searches for input files in DATAPATH. Then, te user provide a list of rRNA sequences in FastA format in test.fasta. This command creates a directory called ribofinder/ where a snakemake pipeline can
sequana_ribofinder –input-directory DATAPATH –rRNA-file test.fasta
You will then need to execute the pipeline:
cd ribofinder sh ribofinder.sh # for a local run
This launch a snakemake pipeline. If you are familiar with snakemake, you can retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters:
snakemake -s ribofinder.rules -c config.yaml --cores 4 --wrapper-prefix git+file:////home/user/sequana_wrappers
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
bowtie1
samtools
pigz
Details
This pipeline runs ribofinder in parallel on the input fastq files. A brief sequana summary report is also produced.
You can start from the reference file and the GFF file. By defaultm we search for the feature called rRNA:
sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff
If the default feature rRNA is not found, no error is raised for now. If you know the expected feature, you can provide it:
sequana_ribofinder --input-directory . --reference-file genome.fasta --gff-file genome.gff --rRNA-feature gene_rRNA
If you have an existing or custom rRNA file, you can then use:
sequana_ribofinder --input-directory . --rRNA-file ribo.fasta
Rules and configuration details
Here is the latest documented configuration file to be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.
Changelog
Version |
Description |
---|---|
0.11.0 |
|
0.10.2 |
|
0.10.1 |
|
0.10.0 |
|
0.9.3 |
|
0.9.2 |
First release. |
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Hashes for sequana_ribofinder-0.11.0.tar.gz
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2548b0e4e1af0a3bf915a40f030951a6f91817cd4be63069bc74fe4501bda280 |
|
MD5 | aaaac42cbaa04b358d14bf9364d06263 |
|
BLAKE2b-256 | b67643e33b257e0004135363c4efeb358dd2ad8899091ada883bfe123c786442 |