7. Applications (standalone)

7.1. Sequanix: GUI for snakemake workflows

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

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.


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.


See also

see Sequanix Tutorial for details

7.2. sequana

Deprecated:will be removed and replaced by Sequanix
Overview:Creates project(s) to run a Sequana pipeline(s)

The sequana executable can be used to create pipelines (and associated config file). For example:

sequana --pipeline quality --file1 R1.fastq.gz --file2 R2.fastq.gz --project TEST

will create a directory called TEST with a few files such as quality.rules, config.yaml, a runme.sh and a README file.

Valid pipelines can be found using:

sequana --show-pipelines

There are many more options and documentation. Please use the --help option for more information.

7.3. sequana_coverage

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

7.4. sequana_summary

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

7.5. sequana_mapping

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

7.6. 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
Sequana:see sequana.kraken
Gallery:see Kraken module example

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

sequana_taxonomy --download toydb

and the official kraken DB (4Gb):

sequana_taxonomy --download minikraken

A database of 8Gb is available. See https://github.com/sequana/data/tree/master/sequana_db1 for instructions and details (bacteria, viruses, human, organelles, …).

7.9. sequana_compressor

Description:standalone on top of the compressor pipeline to compress/decompress FastQ files in different formats, recursively and using multithreaded and multicore tools.

Please see Compressor for details.