tumor tissue-of-origin mapping from plasma
DNA. Nat Genet 49(4):635–642. https://
doi.org/10.1038/ng.3805
- Lin X, Sun D, Rodriguez B, Zhao Q, Sun H,
Zhang Y, Li W (2013) BSeQC: quality control
of bisulfite sequencing experiments. Bioinfor-
matics 29(24):3227–3229. https://doi.org/
10.1093/bioinformatics/btt548
- Sun S, Noviski A, Yu X (2013) MethyQA: a
pipeline for bisulfite-treated methylation
sequencing quality assessment. BMC Bioinfor-
matics 14:259
- Krueger F, Kreck B, Franke A, Andrews SR
(2012) DNA methylome analysis using short
bisulfite sequencing data. Nat Methods 9
(2):145–151
- Adusumalli S, Mohd Omar MF, Soong R,
Benoukraf T (2014) Methodological aspects
of whole-genome bisulfite sequencing analysis.
Brief Bioinform 16(3):369–379.https://doi.
org/10.1093/bib/bbu016
- Xi Y, Li W (2009) BSMAP: whole genome
bisulfite sequence MAPping program. BMC
Bioinformatics 10:232. https://doi.org/10.
1186/1471-2105-10-232
52. Krueger F, Andrews SR (2011) Bismark: a flex-
ible aligner and methylation caller for Bisulfite-
seq applications. Bioinformatics 27
(11):1571–1572. https://doi.org/10.1093/
bioinformatics/btr167
53. Benoukraf T, Wongphayak S, Hadi LH, Wu M,
Soong R (2013) GBSA: a comprehensive soft-
ware for analysing whole genome bisulfite
sequencing data. Nucleic Acids Res 41(4):
e55.https://doi.org/10.1093/nar/gks1281
54. Akalin A, Kormaksson M, Li S, Garrett-
Bakelman FE, Figueroa ME, Melnick A,
Mason CE (2012) methylKit: a comprehensive
R package for the analysis of genome-wide
DNA methylation profiles. Genome Biol 13:
R87
55. Chandrananda D, Thorne NP, Bahlo M (2015)
High-resolution characterization of sequence
signatures due to non-random cleavage of
cell-free DNA. BMC Med Genet 8:29.
https://doi.org/10.1186/s12920-015-0107-
z
56. Efron B, Tibshirani R (1997) Improvements
on cross-validation: the .632+ bootstrap
method. J Am Stat Assoc 92(438):548–560
Bioinformatics Analysis for Cell-Free Tumor DNA Sequencing Data 95
