This is is the revcomp pipeline from the Sequana projet
- Overview:
revert and complement input Fast files
- Input:
A set of FastQ files (paired or single-end) compressed or not
- Output:
A set of reverse completed files
- 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
- Authors:
Thomas Cokelaer
This is is the fastqc pipeline from the Sequana projet
- Overview:
Runs fastqc and multiqc on a set of Sequencing data to produce control quality reports
- Input:
A set of FastQ files (paired or single-end) compressed or not
- Output:
an HTML file summary.html (individual fastqc reports, mutli-samples report)
- Status:
production
- Wiki:
- Documentation:
This README file, the Wiki from the github repository (link above) and https://sequana.readthedocs.io
- Citation:
Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352
Installation
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_revcomp
Usage
sequana_pipelines_revcomp --input-directory DATAPATH
This creates a directory with the pipeline and configuration file. You will then need to execute the pipeline:
cd revcomp sh revcomp.sh # for a local run make clean
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 revcomp.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
Requirements
This pipelines requires the following executable(s):
seqtk
Details
This pipeline runs seqtk in parallel on the input fastq files.
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 |
|---|---|
0.8.4 |
|
0.8.3 |
|
0.8.2 |
Fix schema and rule. output files are now saved in the ./rc directory |
0.8.1 |
Improve the –help message |
0.8.0 |
First version from sequana 0.8.0 |
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
File details
Details for the file sequana_revcomp-0.9.0.tar.gz.
File metadata
- Download URL: sequana_revcomp-0.9.0.tar.gz
- Upload date:
- Size: 8.1 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
twine/4.0.1 CPython/3.7.3
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
cadd25614d5df17dafaa1e6d5e2fbdfeabd32b0d4ff790d7a98d000ae1a60dfd
|
|
| MD5 |
8906174b1f21891bf6278248eb7ef452
|
|
| BLAKE2b-256 |
be8553469d8a50a355a2be20898ef7e37f4fa15e9445070fd7404da79808a134
|
