- Fox EJ, Reid-Bayliss KS, Emond MJ, Loeb LA
(2014) Accuracy of next generation sequenc-
ing platforms. Next Gener Seq Appl 1.https://
doi.org/10.4172/jngsa.1000106 - Arbeithuber B, Makova KD, Tiemann-Boege I
(2016) Artifactual mutations resulting from
DNA lesions limit detection levels in ultrasen-
sitive sequencing applications. DNA Res 23
(6):547–559. https://doi.org/10.1093/
dnares/dsw038 - Lixin Chen PL (2017) DNA damage is a per-
vasive cause of sequencing errors, directly con-
founding variant identification. Science 355
(6326):752–756 - Underhill HR, Kitzman JO, Hellwig S, Welker
NC, Daza R, Baker DN, Gligorich KM, Ros-
tomily RC, Bronner MP, Shendure J (2016)
Fragment length of circulating tumor DNA.
PLoS Genet 12(7):e1006162. https://doi.
org/10.1371/journal.pgen.1006162 - Bolger AM, Lohse M, Usadel B (2014) Trim-
momatic: a flexible trimmer for Illumina
sequence data. Bioinformatics 30
(15):2114–2120. https://doi.org/10.1093/
bioinformatics/btu170 - Chen S, Huang T, Zhou Y, Han Y, Xu M, Gu J
(2017) AfterQC: automatic filtering,
trimming, error removing and quality control
for fastq data. BMC Bioinformatics 18(Suppl
3; 80):91–100. https://doi.org/10.1186/
s12859-017-1469-3 - Langmead B, Salzberg SL (2012) Fast gapped-
read alignment with Bowtie 2. Nat Methods 9
(4):357–359. https://doi.org/10.1038/
nmeth.1923 - Li H, Durbin R (2010) Fast and accurate long-
read alignment with Burrows-Wheeler trans-
form. Bioinformatics 26(5):589–595.https://
doi.org/10.1093/bioinformatics/btp698 - Li H, Handsaker B, Wysoker A, Fennell T,
Ruan J, Homer N, Marth G, Abecasis G,
Durbin R, Genome Project Data Processing S
(2009) The sequence alignment/map format
and SAMtools. Bioinformatics 25
(16):2078–2079. https://doi.org/10.1093/
bioinformatics/btp352 - Tarasov A, Viella AJ, Cuppen E, Nijman IJ,
Prins P (2015) Sambamba: fast processing of
NGS alignment formats. Bioinformatics.
https://doi.org/10.5281/zenodo.13200 - Mose LE, Wilkerson MD, Hayes DN, Perou
CM, Parker JS (2014) ABRA: improved coding
indel detection via assembly-based realign-
ment. Bioinformatics 30(19):2813–2815.
https://doi.org/10.1093/bioinformatics/
btu376 - Garcia-Alcalde F, Okonechnikov K,
Carbonell J, Cruz LM, Gotz S, Tarazona S,
Dopazo J, Meyer TF, Conesa A (2012) Quali-
map: evaluating next-generation sequencing
alignment data. Bioinformatics 28
(20):2678–2679. https://doi.org/10.1093/
bioinformatics/bts503 - McKenna A, Hanna M, Banks E, Sivachenko A,
Cibulskis K, Kernytsky A, Garimella K,
Altshuler D, Gabriel S, Daly M, DePristo MA
(2010) The genome analysis toolkit: a MapRe-
duce framework for analyzing next-generation
DNA sequencing data. Genome Res 20
(9):1297–1303.https://doi.org/10.1101/gr.
107524.110 - Cibulskis K, Lawrence MS, Carter SL,
Sivachenko A, Jaffe D, Sougnez C, Gabriel S,
Meyerson M, Lander ES, Getz G (2013) Sen-
sitive detection of somatic point mutations in
impure and heterogeneous cancer samples. Nat
Biotechnol 31(3):213–219.https://doi.org/
10.1038/nbt.2514 - Koboldt DC, Zhang Q, Larson DE, Shen D,
McLellan MD, Lin L, Miller CA, Mardis ER,
Ding L, Wilson RK (2012) VarScan 2: somatic
mutation and copy number alteration discov-
ery in cancer by exome sequencing. Genome
Res 22(3):568–576. https://doi.org/10.
1101/gr.129684.111 - Wang K, Li M, Hakonarson H (2010) ANNO-
VAR: functional annotation of genetic variants
from high-throughput sequencing data.
Nucleic Acids Res 38(16):e164.https://doi.
org/10.1093/nar/gkq603 - Rausch T, Zichner T, Schlattl A, Stutz AM,
Benes V, Korbel JO (2012) DELLY: structural
variant discovery by integrated paired-end and
split-read analysis. Bioinformatics 28(18):
i333–i339. https://doi.org/10.1093/bioin
formatics/bts378 - Newman AM, Bratman SV, Stehr H, Lee LJ,
Liu CL, Diehn M, Alizadeh AA (2014) FAC-
TERA: a practical method for the discovery of
genomic rearrangements at breakpoint resolu-
tion. Bioinformatics 30(23):3390–3393.
https://doi.org/10.1093/bioinformatics/
btu549 - Wang K, Ma Q, Jiang L, Lai S, Lu X, Hou Y,
Wu CI, Ruan J (2016) Ultra-precise detec-
tion of mutations by droplet-based amplifica-
tion of circularized DNA. BMC Genomics
17:214. https://doi.org/10.1186/s12864-
016-2480-1 - Schmieder R, Edwards R (2011) Quality con-
trol and preprocessing of metagenomic data-
sets. Bioinformatics 27(6):863–864.https://
doi.org/10.1093/bioinformatics/btr026
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