Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

BMC Bioinformatics

Volumn 17, Issue 1, 2016, Pages

  Girardot, Charles ^a   Scholtalbers, Jelle ^a   Sauer, Sajoscha ^a   Su, Shu Yi ^a   Furlong, Eileen E M ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Duplicates; Genomics; Multiplexing; NGS; Software; UMI

Indexed keywords

COMPUTER SOFTWARE; DNA SEQUENCES; GALAXIES; GENE ENCODING; MULTIPLEXING; NUCLEIC ACIDS; POLYMERASE CHAIN REACTION;

CODE DEVELOPMENT; COMMON PRACTICES; DUPLICATES; GENOMICS; NEXT GENERATION SEQUENCERS; RANDOM SEQUENCE; RNA SEQUENCING; SINGLE CELLS;

BAR CODES;

DNA SEQUENCE; GENE LIBRARY; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; INFORMATION PROCESSING; POLYMERASE CHAIN REACTION; PROCEDURES;

AUTOMATIC DATA PROCESSING; GENE LIBRARY; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84990841832     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-016-1284-2     Document Type: Article

References (20)

1. Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet. 2014;15(2):121-32.
2. The FASTX-toolkit. http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 30 Nov 2015.
3. ea-utils. https://expressionanalysis.github.io/ea-utils/. Accessed 30 Nov 2015.
4. Kivioja T, Vähärautio A, Karlsson K, Bonke M, Enge M, Linnarsson S, et al. Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods. 2011;9:72-4.
5. Shiroguchi K, Jia TZ, Sims PA, Xie XS. Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes. Proc Natl Acad Sci U S A. 2012;109(4):1347-52.
6. Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA. Detection of ultra-rare mutations by next-generation sequencing. Proc Natl Acad Sci U S A. 2012;109(36):14508-13.
7. Stegle O, Teichmann SA, Marioni JC. Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. 2015;16(3):133-45.
8. Picard. http://broadinstitute.github.io/picard/. Accessed 30 Nov 2015.
9. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5.
10. Blankenberg D, Von Kuster G, Bouvier E, Baker D, Afgan E, Stoler N, et al. Dissemination of scientific software with Galaxy ToolShed. Genome Biol. 2014;15(2):403.
11. Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG. Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods. 2013;10(11):1093-5.
12. Islam S, Zeisel A, Joost S, La Manno G, Zajac P, Kasper M, Lönnerberg P, Linnarsson S. Quantitative single-cell RNA-seq with unique molecular identifiers. Nat Methods. 2014;11(2):163-6.
13. Zarnack K, Konig J, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM, Ule J. Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements. Cell. 2013;152(3):453-66.
14. Renaud G, Stenzel U, Maricic T, Wiebe V, Kelso J. deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. Bioinformatics. 2015;31(5):770-2.
15. Yi H, Li Z, Li T, Zhao J. Bayexer: an accurate and fast Bayesian demultiplexer for Illumina sequences. Bioinformatics. 2015;31(24):4000-2.
16. Costea PI, Lundeberg J, Akan P. TagGD: fast and accurate software for DNA Tag generation and demultiplexing. PLoS One. 2013;8(3):e57521.
17. Herten K, Hestand MS, Vermeesch JR, Van Houdt JK. GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. BMC Bioinformatics. 2015;16:73.
18. Dodt M, Roehr JT, Ahmed R, Dieterich C. FLEXBAR-Flexible Barcode and Adapter Processing for Next-Generation Sequencing Platforms. Biology (Basel). 2012;1(3):895-905.
19. Smith TS, Heger A, Sudbery I. UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. doi:http://dx.doi.org/ 10.1101/051755.
20. Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, Mamedov IZ, Tuganbaev TR, Bolotin DA, Staroverov DB, Putintseva EV, Plevova K, Linnemann C, Shagin D, Pospisilova S, Lukyanov S, Schumacher TN, Chudakov DM. Towards error-free profiling of immune repertoires. Nat Methods. 2014;11(6):653-5.