Package: sequana-coverage
This is is thecoveragepipeline from theSequanaprojetOverview:Parallelised version of sequana_coverage for large eukaryotes genome.Input:A set of BAM or BED files. BED file must have 3 or 4 columns. First column is
the chromosome/contig name, second column stored positions and third the
coverage. Fourth optional columns contains a filtered coverage (not used in
the analysis but shown in the HTML reports)Output:a set of HTML reports for each chromosomes and a multiqc reportStatus:productionCitation:Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas CokelaerSequana coverage: detection and characterization of genomic variations
using running median and mixture modelsGigaScience, Volume 7, Issue 12, December 2018, giy110,https://doi.org/10.1093/gigascience/giy110andCokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOIhttps://doi:10.21105/joss.00352InstallationYou must install Sequana first:pip install sequanaThen, just install this package:pip install sequana_coverageThis gives an executable called sequana_pipelines_coverage. Note that is should
not be confused with the original sequana_coverage standalone from Sequana
library. Indeed, this pipeline calls sequana_coverage behund the scene.Usagesequana_pipelines_coverage --help
sequana_pipelines_coverage --input-directory DATAPATHBy default, this looks for BED file. WARNING. This are BED3 meaning a 3-columns
tabulated file like this one:chr1 1 10
chr1 2 11
...
chr1 N1 10
chr2 1 20
chr2 2 21
...
chr2 N2 20where the first column stored the chromosome name, the second is the position
and the third is the coverage itself. See sequana_coverage documentation for
details. If you have BAM files as input, we will do the conversion for you. In
such case, use this option:--input-pattern "*.bam"The sequana_pipelines_coverage script creates a directory with the pipeline and
its configuration file. You will then need
to execute the pipeline:cd coverage
sh coverage.sh  # for a local runThis 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 coverage.rules -c config.yaml --cores 4 --stats stats.txtOr usesequanixinterface as follows:sequanix -w analysis -i . -p coverageGo to the second panel, in Input data and then in Input directory. There, you
must modify the pattern (empty field by default meaning search for fastq files)
and set the field to either:*.bedor:*.bamYou are ready to go. Save the project and press Run. Once done, open the HTML report.RequirementsThis pipelines requires the following executable(s):sequana_coverage fromSequana, which should be installed automatically.multiqcDetailsThis pipeline runscoveragein parallel on the input BAM files (or BED file).The coverage tool takes as input a BAM or a BED file. The BED file must have 3
or 4 columns as explained in the standalone application (sequana_coverage)documentation.
In short, the first column is the chromosome name, the second column is the
position (sorted) and the third column is the coverage (an optional fourth
column would contain a coverage signal, which could be high quality coverage for
instance).If you have only BAM files, you can convert them usingbioconverttool or
the command:samtools depth -aa input.bam > output.bedIf you have a CRAM file:samtools view -@ 4 -T reference.fa -b -o out.bam  in.cramFor very large BAM/BED files, we recommend to split the BED file by
chromosomes. For instance for the chromosome  chr1, type:# samtools index in.bam
samtools depth -aa input.bam -r chr1 in.bam > chr1.bedThe standalone or Snakemake application can also take as input your BAM file and
will convert it automatically into a BED file.Rules and configuration detailsHere is thelatest documented configuration fileto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file.ChangelogVersionDescription0.9.1rename genbank field into annotation, window into window_size0.9.0first version