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Items: 1 to 20 of 96

1.

De novo clustering of long reads by gene from transcriptomics data.

Marchet C, Lecompte L, Silva CD, Cruaud C, Aury JM, Nicolas J, Peterlongo P.

Nucleic Acids Res. 2019 Jan 10;47(1):e2. doi: 10.1093/nar/gky834.

2.

Genome assembly using Nanopore-guided long and error-free DNA reads.

Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM.

BMC Genomics. 2015 Apr 20;16:327. doi: 10.1186/s12864-015-1519-z.

3.

MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach.

Brown BL, Watson M, Minot SS, Rivera MC, Franklin RB.

Gigascience. 2017 Mar 1;6(3):1-10. doi: 10.1093/gigascience/gix007.

4.

Challenges and advances for transcriptome assembly in non-model species.

Ungaro A, Pech N, Martin JF, McCairns RJS, Mévy JP, Chappaz R, Gilles A.

PLoS One. 2017 Sep 20;12(9):e0185020. doi: 10.1371/journal.pone.0185020. eCollection 2017.

5.

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing.

Qu W, Hashimoto S, Morishita S.

Genome Res. 2009 Jul;19(7):1309-15. doi: 10.1101/gr.089151.108. Epub 2009 May 13.

6.

MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome.

Tyson JR, O'Neil NJ, Jain M, Olsen HE, Hieter P, Snutch TP.

Genome Res. 2018 Feb;28(2):266-274. doi: 10.1101/gr.221184.117. Epub 2017 Dec 22.

7.

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.

Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C, Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J, Aury JM.

Gigascience. 2017 Feb 1;6(2):1-13. doi: 10.1093/gigascience/giw018.

8.

Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens.

Deschamps S, Mudge J, Cameron C, Ramaraj T, Anand A, Fengler K, Hayes K, Llaca V, Jones TJ, May G.

Sci Rep. 2016 Jun 28;6:28625. doi: 10.1038/srep28625.

9.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

10.

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes.

Srivastava A, Sarkar H, Gupta N, Patro R.

Bioinformatics. 2016 Jun 15;32(12):i192-i200. doi: 10.1093/bioinformatics/btw277.

11.

Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.

Ptitsyn A, Temanni R, Bouchard C, Anderson PA.

PLoS One. 2015 Sep 22;10(9):e0138006. doi: 10.1371/journal.pone.0138006. eCollection 2015.

12.

High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads.

Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T.

J Biotechnol. 2017 Sep 20;258:197-205. doi: 10.1016/j.jbiotec.2017.04.016. Epub 2017 Apr 19.

PMID:
28433722
13.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

14.

Assessing the performance of the Oxford Nanopore Technologies MinION.

Laver T, Harrison J, O'Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ.

Biomol Detect Quantif. 2015 Mar;3:1-8.

15.

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome.

Goodwin S, Gurtowski J, Ethe-Sayers S, Deshpande P, Schatz MC, McCombie WR.

Genome Res. 2015 Nov;25(11):1750-6. doi: 10.1101/gr.191395.115. Epub 2015 Oct 7.

16.

EasyCluster2: an improved tool for clustering and assembling long transcriptome reads.

Bevilacqua V, Pietroleonardo N, Giannino E, Stroppa F, Simone D, Pesole G, Picardi E.

BMC Bioinformatics. 2014;15 Suppl 15:S7. doi: 10.1186/1471-2105-15-S15-S7. Epub 2014 Dec 3.

17.

PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms.

Gan RC, Chen TW, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P.

BMC Bioinformatics. 2016 Dec 22;17(Suppl 19):513. doi: 10.1186/s12859-016-1366-1.

18.

Accurate identification and analysis of human mRNA isoforms using deep long read sequencing.

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M.

G3 (Bethesda). 2013 Mar;3(3):387-97. doi: 10.1534/g3.112.004812. Epub 2013 Mar 1.

19.

TransFlow: a modular framework for assembling and assessing accurate de novo transcriptomes in non-model organisms.

Seoane P, Espigares M, Carmona R, Polonio Á, Quintana J, Cretazzo E, Bota J, Pérez-García A, Dios Alché J, Gómez L, Claros MG.

BMC Bioinformatics. 2018 Nov 20;19(Suppl 14):416. doi: 10.1186/s12859-018-2384-y.

20.

The long reads ahead: de novo genome assembly using the MinION.

de Lannoy C, de Ridder D, Risse J.

Version 2. F1000Res. 2017 Jul 7 [revised 2017 Jan 1];6:1083. doi: 10.12688/f1000research.12012.2. eCollection 2017. Review.

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