561 related articles for article (PubMed ID: 22808927)
1. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.
Haznedaroglu BZ; Reeves D; Rismani-Yazdi H; Peccia J
BMC Bioinformatics; 2012 Jul; 13():170. PubMed ID: 22808927
[TBL] [Abstract][Full Text] [Related]
2. Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.
Mbandi SK; Hesse U; van Heusden P; Christoffels A
BMC Bioinformatics; 2015 Feb; 16(1):58. PubMed ID: 25880035
[TBL] [Abstract][Full Text] [Related]
3. Comparison of De Novo Transcriptome Assemblers and k-mer Strategies Using the Killifish, Fundulus heteroclitus.
Rana SB; Zadlock FJ; Zhang Z; Murphy WR; Bentivegna CS
PLoS One; 2016; 11(4):e0153104. PubMed ID: 27054874
[TBL] [Abstract][Full Text] [Related]
4. Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers.
Amin S; Prentis PJ; Gilding EK; Pavasovic A
BMC Res Notes; 2014 Aug; 7():488. PubMed ID: 25084827
[TBL] [Abstract][Full Text] [Related]
5. Comprehensive evaluation of de novo transcriptome assembly programs and their effects on differential gene expression analysis.
Wang S; Gribskov M
Bioinformatics; 2017 Feb; 33(3):327-333. PubMed ID: 28172640
[TBL] [Abstract][Full Text] [Related]
6. 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; 12(9):e0185020. PubMed ID: 28931057
[TBL] [Abstract][Full Text] [Related]
7. Grouper: graph-based clustering and annotation for improved de novo transcriptome analysis.
Malik L; Almodaresi F; Patro R
Bioinformatics; 2018 Oct; 34(19):3265-3272. PubMed ID: 29746620
[TBL] [Abstract][Full Text] [Related]
8. The complex task of choosing a de novo assembly: lessons from fungal genomes.
Gallo JE; Muñoz JF; Misas E; McEwen JG; Clay OK
Comput Biol Chem; 2014 Dec; 53 Pt A():97-107. PubMed ID: 25262360
[TBL] [Abstract][Full Text] [Related]
9. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes.
Johnson LK; Alexander H; Brown CT
Gigascience; 2019 Apr; 8(4):. PubMed ID: 30544207
[TBL] [Abstract][Full Text] [Related]
10. Evaluation of short read metagenomic assembly.
Charuvaka A; Rangwala H
BMC Genomics; 2011; 12 Suppl 2(Suppl 2):S8. PubMed ID: 21989307
[TBL] [Abstract][Full Text] [Related]
11. 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; 17(Suppl 19):513. PubMed ID: 28155708
[TBL] [Abstract][Full Text] [Related]
12. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.
Zhao QY; Wang Y; Kong YM; Luo D; Li X; Hao P
BMC Bioinformatics; 2011 Dec; 12 Suppl 14(Suppl 14):S2. PubMed ID: 22373417
[TBL] [Abstract][Full Text] [Related]
13. Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.
García-López R; Vázquez-Castellanos JF; Moya A
Front Bioeng Biotechnol; 2015; 3():141. PubMed ID: 26442255
[TBL] [Abstract][Full Text] [Related]
14. Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.
Yang Y; Smith SA
BMC Genomics; 2013 May; 14():328. PubMed ID: 23672450
[TBL] [Abstract][Full Text] [Related]
15. A pipeline for the de novo assembly of the Themira biloba (Sepsidae: Diptera) transcriptome using a multiple k-mer length approach.
Melicher D; Torson AS; Dworkin I; Bowsher JH
BMC Genomics; 2014 Mar; 15(1):188. PubMed ID: 24621177
[TBL] [Abstract][Full Text] [Related]
16. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.
Feldmeyer B; Wheat CW; Krezdorn N; Rotter B; Pfenninger M
BMC Genomics; 2011 Jun; 12():317. PubMed ID: 21679424
[TBL] [Abstract][Full Text] [Related]
17. Comparative performance of transcriptome assembly methods for non-model organisms.
Huang X; Chen XG; Armbruster PA
BMC Genomics; 2016 Jul; 17():523. PubMed ID: 27464550
[TBL] [Abstract][Full Text] [Related]
18. Combining transcriptome assemblies from multiple de novo assemblers in the allo-tetraploid plant Nicotiana benthamiana.
Nakasugi K; Crowhurst R; Bally J; Waterhouse P
PLoS One; 2014; 9(3):e91776. PubMed ID: 24614631
[TBL] [Abstract][Full Text] [Related]
19. Reconstruction of Acetogenesis Pathway Using Short-Read Sequencing of Clostridium aceticum Genome.
Lee S; Song Y; Choe D; Cho S; Yu SJ; Cho Y; Kim SC; Cho BK
J Nanosci Nanotechnol; 2015 May; 15(5):3852-61. PubMed ID: 26505015
[TBL] [Abstract][Full Text] [Related]
20. A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing.
Hoang NV; Furtado A; Mason PJ; Marquardt A; Kasirajan L; Thirugnanasambandam PP; Botha FC; Henry RJ
BMC Genomics; 2017 May; 18(1):395. PubMed ID: 28532419
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]