Table 1.

List of the different packages and main modules. If any other modules exist but are not presented here, multiple dots are shown

Packages (nb of modules)	Modules	Functions
bwa (5)	bwaIndex	Indexing the reference Fasta file
	bwaAln	Create the alignment for FASTQ sequences
	bwaSampe	Create the SAM file for pair-end sequences
	bwaSamse	Create the SAM file for single-end sequences
	...	...
cutadapt (2)	CreateConfFile	Create the specific cutadapt configuration file
	execution	Execute cutadapt command
fastqc (6)	execution	Run FastQC software
	parse	Parse the FastQC results
	...	...
gatk (8)	gatkVariantFiltrator	Filter the different SNP based on specific options
	gatkHaplotypeCaller	Call the haplotype of each individual based on a BAM file
	...	...
pairing (4)	pairRecognition	Allow the recognition of pairs in a set of FASTQ files
	repairing	Reorganize in pair two FASTQ files, extract single sequences
picardTools (3)	picardToolsMarkDuplicates	Mark/eliminate different types of duplicate in a BAM file
	picardToolsCreateSequenceDictionnary	Create the “.dict” file of the reference
	picardToolsSortSam	Sort the SAM file
	...	...
samTools (10)	samToolsSort	Sort the SAM/BAM file
	samToolsIndex	Index the SAM/BAM file
	mergeHeader	Merge the header of multiples SAM/BAM into a single one
	...	...
toolbox (73)	exportLog	Export information into log files
	checkFile	Check if a file exists, is readable/writable, and is not empty
	existsDir	Check if a directory exists
	makeDir	Create a new directory
	readDir	Read the content of a directory
	extractPath	Extract the complete path of a file
	extractName	Create a readgroup from a file name
	readFileConf	Read the configuration file and return a hash
	extractOptions	Provide the options for a given software from the hash
	run	Run the command line given in argument
	checkSamOrBamFormat	Check if a file is a true SAM/BAM format
	extractHashSoft	Extract specific options for a given tool
	checkNumberByWC	Provide the number of sequence in a given FASTQ file
	checkEncodeByASCIIcontrol	Check the format of encoding in a FASTQ file
	changeEncode	Provide a wrapper to change the encoding of a FASTQ file
	...	...