TransRate protocols

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TransRate specifications

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Unique identifier OMICS_09086
Name TransRate
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R, Ruby
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for TransRate

TransRate in pipelines

 (17)
2017
PMCID: 5264399
PMID: 28120863
DOI: 10.1038/srep40788

[…] process. therefore, in order to evaluate the quality of the produced assembly, sequenced reads were mapped back to the reference assembly and quantitative and qualitative measures were applied using transrate. a redundancy filter was then applied using cd-hit-est v 4.6.4 to remove contigs with more than 95% similarity. to evaluate the transcriptome completeness, cdna and peptide collections […]

2017
PMCID: 5282741
PMID: 28143409
DOI: 10.1186/s12864-017-3505-0

[…] for each species and then refined with program to assemble spliced alignments (pasa). the completeness and quality were assessed with the benchmarking universal single-copy orthologs (busco) and transrate tools at each stage of the assemblies. the final datasets of 11,315-12,849 transcripts contained 5,610-7,712 updates and corrections to >50% of existing gene models including changes […]

2017
PMCID: 5301240
PMID: 28186107
DOI: 10.1038/srep42110

[…] contigs (or “transcripts”) in 391,055 “gene families.” the size of the assembly was 716 mbases., assembly quality statistics obtained according to current recommendations are shown in . the overall transrate quality score for the assembly was 0.42 (on a scale of 0 to 1), which is higher than >50% of the transcriptomes deposited in the ncbi transcriptome shotgun assembly database. read […]

2017
PMCID: 5322684
PMID: 28250805
DOI: 10.1186/s13015-017-0091-2

[…] make use of annotated reference genomes to assess if our predictions are correct. we compared our measure against two state-of-the-art methods for de novo transcriptome evaluation, rsem-eval [] and transrate [], on the specific task of identifying chimeric transcripts in trinity’s assemblies on all four described datasets. in all our tests, we used the contig impact score of rsem-eval […]

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] <0.5), were filtered out of the dataset. the resultant assembly was annotated using the software package dammit (https://github.com/camillescott/dammit), and evaluated using busco 2.0 beta 3 and transrate version 1.0.1., all samples were used (20 hypothalamus (11 male, 9 female), 23 pituitary (14 male, 9 female), 13 testes, and 10 ovary samples from 24 birds.) raw reads were mapped […]


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TransRate in publications

 (40)
PMCID: 5945926
PMID: 29780371
DOI: 10.3389/fmicb.2018.00859

[…] filtered reads from all 12 rhizosphere libraries was combined into a single reference transcriptome assembly. assembly and contig quality analysis was performed using both trinity scripts and transrate (smith-unna et al., ). the assembly was annotated using trinotate (bryant et al., ). transcripts were subjected to a blastx search (e ≤ 1e−5) of the protein database swiss-prot (boeckmann […]

PMCID: 5794766
PMID: 29391456
DOI: 10.1038/s41598-018-20416-y

[…] minlen:25). sequences shorter 25 bp were discarded. the transcriptome de novo assembly was performed using trinity (v.2.3.2.). various assembly combinations were performed and analyzed by transrate (v1.0.3.). resulting transcripts were aligned with the ncbi nr database by blastx search with an e-value cutoff of 1 × 10−4. the resulting blast hits were processed using blast2go software […]

PMCID: 5730564
PMID: 29242515
DOI: 10.1038/s41467-017-02214-8

[…] units transcribe 72,846 genes, of which 44,328 are non-redundant, 38.8% are trans-spliced and 79.98% have an experimentally defined poly(a) site (table  ). the non-redundant transcriptome has transrate scores of 0.4360 and 0.4797 for transcriptional units and gene sequences, respectively, positioning it among the highest quality transcriptome assemblies. the transcriptome is 98.1% […]

PMCID: 5727884
PMID: 29233089
DOI: 10.1186/s12870-017-1187-z

[…] provided with the trinity package. busco (benchmarking universal single-copy orthologs) was used to explore completeness of the transcriptome according to conserved ortholog content []. finally, transrate was used to compare the assembly to the publicly available cucumis sativus protein-coding primary transcript sequences []., the de novo-assembled transcripts were compared […]

PMCID: 5716010
PMID: 29206218
DOI: 10.1038/sdata.2017.178

[…] rf as read orientation for a strand-specific assembly. in addition, as a complementary resource, de novo transcriptome assemblies for each of the two sampling localities were also performed. transrate v1.0.3 was used to evaluate assembly quality and completeness and to remove possible chimeras and poorly supported contigs. cleaned reads were mapped back to the produced assembly […]


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TransRate institution(s)
Department of Plant Sciences, University of Cambridge, Downing Street, UK; Department of Computer Science, Stony Brook University, Stony Brook, NY, USA; Department of Plant Sciences, University of Oxford, UK

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