@article{fdi:010065444,
  title = {{TOGGLE} : toolbox for generic {NGS} analyses},
  author = {{M}onat, {C}{\'e}cile and {D}ubreuil {T}ranchant, {C}hristine and {K}ougbeadjo, {A}. and {F}arcy, {C}. and {O}rtega-{A}bboud, {E}. and {A}manzougarene, {S}. and {R}avel, {S}. and {A}gbessi, {M}. and {O}rjuela-{B}ouniol, {J}. and {S}ummo, {M}. and {S}abot, {F}ran{\c{c}}ois},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}he explosion of {NGS} ({N}ext {G}eneration {S}equencing) sequence data requires a huge effort in {B}ioinformatics methods and analyses. {T}he creation of dedicated, robust and reliable pipelines able to handle dozens of samples from raw {FASTQ} data to relevant biological data is a time-consuming task in all projects relying on {NGS}. {T}o address this, we created a generic and modular toolbox for developing such pipelines. {R}esults: {TOGGLE} ({TO}olbox for {G}eneric n{G}s ana{L}ys{E}s) is a suite of tools able to design pipelines that manage large sets of {NGS} softwares and utilities. {M}oreover, {TOGGLE} offers an easy way to manipulate the various options of the different softwares through the pipelines in using a single basic configuration file, which can be changed for each assay without having to change the code itself. {W}e also describe one implementation of {TOGGLE} in a complete analysis pipeline designed for {SNP} discovery for large sets of genomic data, ready to use in different environments (from a single machine to {HPC} clusters). {C}onclusion: {TOGGLE} speeds up the creation of robust pipelines with reliable log tracking and data flow, for a large range of analyses. {M}oreover, it enables {B}iologists to concentrate on the biological relevance of results, and change the experimental conditions easily.},
  keywords = {{NGS} ; {T}oolbox ; {P}ipeline ; {F}lexible},
  booktitle = {},
  journal = {{B}mc {B}ioinformatics},
  volume = {16},
  numero = {},
  pages = {art. 374 [8 ]},
  ISSN = {1471-2105},
  year = {2015},
  DOI = {10.1186/s12859-015-0795-6},
  URL = {https://www.documentation.ird.fr/hor/fdi:010065444},
}