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 Ma^1#

• 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: [email protected]

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.