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

From: TOGGLE: toolbox for generic NGS analyses

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
  ... ...