how_to_cite.txt

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### CITATION
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Please cite the follows softwares:

#Trimmomatic
  'Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics, btu170.'


#MultiQC
  'MultiQC: Summarize analysis results for multiple tools and samples in a single report', 'Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller','Bioinformatics (2016)','doi: 10.1093/bioinformatics/btw354', 'PMID: 27312411'


#FastQC
  'Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc'


#STAR
  'Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R. Gingeras, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, Volume 29, Issue 1, January 2013, Pages 15–21, https://doi.org/10.1093/bioinformatics/bts635'
  
  
#Hisat2
  'Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 2015'
  
  
#featureCounts
  'Liao Y, Smyth GK and Shi W (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7):923-30.'
  
  
#HTSeqCount
  'Simon Anders, Paul Theodor Pyl, Wolfgang Huber, HTSeq — A Python framework to work with high-throughput sequencing data
Bioinformatics (2014), in print, online at doi:10.1093/bioinformatics/btu638'


#BAQCOM
  OLIVEIRA, H.C. & CANTAO, M.E.(2019). BAQCOM: Bioinformatics Analysis for Quality Control and Mapping. Available online at: https://github.com/hanielcedraz/BAQCOM