/SequencErr

Supplementary data and codes used to generate figures for SequencErr paper

Supplementary data and codes for

SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data

Eric M Davis*1, Yu Sun*1,2, Yanling Liu*1, Pandurang Kolekar1, Ying Shao1, Karol Szlachta1, Heather L Mulder1, Dongren Ren3, Stephen V Rice1, Zhaoming Wang4, Joy Nakitandwe5, Alex Gout1, Bridget Shaner1, Salina Hall6,Leslie L Robison4, Stanley Pounds7, Jefferey Klco5, John Easton1, Xiaotu Ma1#

  • 1 Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN

  • 2 Department of Computer Science, University of Memphis, Memphis, TN

  • 3 Independent Researcher, Memphis, TN

  • 4 Department of Epidemiology & Cancer Control, St. Jude Children's Research Hospital, Memphis, TN

  • 5 Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN

  • 6 Discovery Life Sciences, Huntsville, AL

  • 7 Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN

  • # To whom correspondence should be addressed: Xiaotu.Ma@stjude.org

SequencErr

SequencErr app is available on St. Jude Cloud at https://platform.stjude.cloud/workflows/sequencerr for non-profit research uses.

Citation

Davis, E.M. et al. SequencErr: measuring and suppressing sequencer errors in next-generation sequencing data. Genome Biol 22, 37 (2021). https://doi.org/10.1186/s13059-020-02254-2

Requirements

Following packages and their respective dependencies should be installed before using the R scripts in this repository. At the time of analysis R v3.6.1 was used to generate the figures.

  • beeswarm
  • ggpubr
  • pheatmap
  • RColorBrewer
install.packages(c('beeswarm', 'ggpubr', 'pheatmap', 'RColorBrewer'), repos = 'http://cran.us.r-project.org', dependencies = TRUE)

Data

Unzip the archives analysis.zip and data.zip

Please find pairerror data used in this study in the folder data/pairerror.

Figures

All figures and related codes can be found in the folder analysis:

  1. Fig1.e,f,g: Fig1_flowcell/heatmap/*pdf
  2. Fig2.a,b and FigS2: in Fig2ab_S2_cross_platform_instrument_comparison/*pdf
  3. Fig2.c,d: Fig2cd_compare_surface/*pdf
  4. Fig3 and FigS6-8: Fig3_S678_COLO829/*pdf
  5. FigS1 and FigS3: FigS13/*pdf
  6. FigS4 and FigS5: FigS45/*pdf

Codes and input data

R codes and input data for each figure can be found in the same folder as figure with similar names.