sequana-downsampling 0.9.0

Description:

sequanadownsampling 0.9.0

This is is the downsampling pipeline from the Sequana project

Overview:
downsample NGS data sets

Input:
a set of FastQ or FASTA files

Output:
a set of downsampled files

Status:
production

Citation(sequana):
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

Citation(pipeline):




Installation
You must install Sequana first:
pip install sequana
Then, just install this package:
pip install sequana_downsampling


Usage
sequana_downsampling --help
sequana_downsampling --input-directory DATAPATHH
sequana_downsampling --downsampling-method random --downsampling-max-entries 100
sequana_downsampling --downsampling-method random_pct --downsampling-percent 10 --downsampling-input-format fasta --input-pattern "whatever*fasta"
Note that the current implementation handles fastq files (zipped or not) and
fasta files (uncompressed only)
This creates a directory with the pipeline and configuration file. You will then need
to execute the pipeline:
cd downsampling
sh downsampling.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 downsampling.rules -c config.yaml --cores 4 --stats stats.txt
Or use sequanix interface.
Examples of a set of FastQ zipped files in the current directory:

sequana_downsampling –run –downsampling-method random_pct
cd downsampling
make clean

This will create a directory called downsampling, and randomly select 10% of
the input reads for each file with extension .fastq.gz in the current directory.
Since -run is used, the pipeline is executed automatically. The following
commands will enter into the directory and called a Makefile. This will clean
the directory for temporary files.


Requirements
This pipelines requires the following executable(s):

sequana
pigz



Details
This pipeline runs downsampling in parallel on the input fastq or fasta files (paired or not). If paired, the one-to-one mapping is conserved.
It can take as input a set of FastQ files, or FastA files. by
default, the pipeline with randomly select 1000 entries from each input files.
You can increase this number using –downsampling-max-entries option. If you
prefer to select a percentage of the entries instead, you can change the
downsamping method as follows:
--downsampling-method random_pct
and change the value if needed (default is 10%):
--downsampling-percent 20
Note that input FastQ can be gzipped. Output files are gzipped. FastA input
files must be compressed for now


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



0.8.5

cope with R1/R2 paired data properly. Improved make file



0.8.4

add missing MANIFEST to include missing requirements.txt



0.8.3

comply with new API from sequana_pipetools 0.2.4



0.8.2

add a –run option to execute the pipeline directly



0.8.1

fix input and N in the random selection



0.8.0
First release.