Table 1 List of the different packages and main modules. If any other modules exist but are not presented here, multiple dots are shown

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

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cutadapt (2)

CreateConfFile

Create the specific cutadapt configuration file

execution

Execute cutadapt command

fastqc (6)

execution

Run FastQC software

parse

Parse the FastQC results

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gatk (8)

gatkVariantFiltrator

Filter the different SNP based on specific options

gatkHaplotypeCaller

Call the haplotype of each individual based on a BAM file

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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

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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

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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

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