sequana-ribofinder 1.2.0

A multi-sample identification of ribosomal content

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

Using pip from Python, just install this package:

pip install sequana_ribofinder --upgrade

The –upgrade option is to make sure you’ll get the latest version.

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):

• bowtie2 >= 2.4.0

• bwa

• sambamba

• bedtools

• samtools

• pigz

The aligner is selectable at the command line with --aligner bowtie2 (default) or --aligner bwa. You only need to install the one(s) you intend to use.

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 default we search for the feature called rRNA to be found in the GFF file:

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 though:

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 it as follows, in which case, no input reference is required:

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
1.2.0	Replace bowtie1 with bowtie2 (default) and bwa as aligner options for rRNA mapping; the aligner is now user-selectable via --aligner bowtie2|bwa. Drop the bowtie1-specific fix_bowtie1_log workaround and the standalone bam_indexing / samtools_faidx rules; the new sequana-wrappers already produce sorted+indexed BAMs and a faidx’ed reference. For bwa, feed multiqc with samtools stats output (bwa has no native multiqc module); the mapping-rate plot in the HTML report is built from multiqc_samtools_stats.txt. For bowtie2, the HTML summary uses sequana.multiqc.plots.Bowtie2 which handles both single-end and paired-end outputs. Rewrite the HTML summary introduction to explain what the pipeline does, how it works step-by-step, and how to interpret each of the three plots (mapping rate, per-sequence proportions, per-sequence RPKM). (bowtie2, bwa, sambamba replace bowtie/bamtools).
1.1.1	hotfix for running on HPC (slurm)
1.1.0	Uses click (refactoring of sequana_pipetools)
1.0.1	add sequana_wrappers in the config/pipeline
1.0.0	use graphviz apptainer and latest wrappers
0.13.0	add final apptainers and update CI actions
0.12.0	set singularity containers
0.11.1	Fix config file (removing hard-coded path)
0.11.0	Fix multiqc plot using same fix as in sequna_rnaseq pipelines add utility plot to check rate of ribosomal per sequence and also the corresponding RPKM.
0.10.2	Fix the bowtie1 rule (all samples were named bowtie1)
0.10.1	add additional test and fix bug in pipeline (regression bug)
0.10.0	Update to use sequana-wrappers. Remove multiqc. summary.html is self-content
0.9.3	fix logger
0.9.2	First release.