7. Applications (standalone)

7.1. Sequanix: GUI for snakemake workflows

Overview:

a Graphical User Interface (GUI) for Sequana pipelines and any Snakemake-based workflows.

Status:

Production

Name:

sequanix

This GUI can be used to load Snakefile and their configuration file. A working directory has to be set. Once done, the configuration file can be changed in the GUI. Finally, one can run the snakefile and see the progress. Tooltips are automatically created from the configuration file (if documented).

Since snakemake has the ability to run jobs locally or on a cluster, this application can also be run either locally or a distributed computing platform (e.g., cluster with slurm scheduler). Of course, this means you can use a X environment on your cluster (ssh -X should do it).

Just type sequanix in a shell.

Note

tested under Linux only. However, Mac and Windows users should be able to use it since it is based on Python and PyQt. Again, we strongly advice to use Anaconda to install all required dependencies

Here is a snapshot.

_images/sequanix.png

See also

see Sequanix Tutorial for details

7.2. sequana_coverage

Description:

Show coverage and interval of confidence to identify under and over represented genomic regions.

Status:

Production

Help:

please use sequana_coverage --help

Sequana:

See GenomeCov to use the coverage in your own script.

Gallery:

See examples in the gallery

Starting from a BED file and its reference, one can use this command in a shell:

sequana_coverage  --input JB409847.sorted.bed -o
                  --reference JB409847.fa --show-html

It creates an HTML report with various images showing the coverage and GC versus coverage plots. It also provides a set of CSV files with low or high coverage regions (as compared to the average coverage).

See also

the underlying algorithm is described in details in the documentation (sequana.bedtools.GenomeCov).

7.3. sequana_summary

Description:

Prints basic statistics about a set of NGS input files. Currently handles Fastq (gzipped or not) or BED files (coverage).

Usage:

sequana summary file1.fastq.gz

7.4. sequana_mapping

Description:

a simple application to map reads onto a genome given one or two FastQ files (gzipped) and a reference.

sequana_mapping --file1 H1_R1.fastq.gz --file2 H1_R2.fastq.gz --reference temp.fa

will map all reads on the reference using bwa.

7.5. sequana_taxonomy

Description:

Creates a HTML document with Krona and pie chart of taxonomic content of a FastQ file (paired or not). Uses Kraken, Krona and a dedicated Sequana database.

Help:

sequana_taxonomy --help

Status:

Production

Sequana:

see sequana.kraken

Gallery:

see Kraken module example

You will need to download databases. We provide a toy example:

sequana_taxonomy --download toydb