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rnaQUAST specifications

Information


Unique identifier OMICS_11513
Name rnaQUAST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data rnaQUAST takes assembled transcripts as an input and maps them to the reference genome using either BLAT or GMAP.
Operating system Unix/Linux
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2.0
Stability Stable
Requirements
GMAP (or BLAT), BLASTN, gffutils, matplotlib
Maintained Yes

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Maintainer


  • person_outline Andrey D. Prjibelski <>

Publication for rnaQUAST

rnaQUAST in pipeline

2017
PMCID: 5597892
PMID: 28873961
DOI: 10.1093/gigascience/gix057

[…] total length of transcripts, n50 length, mean length, proportion of mapped reads, and number of transcripts whose length was larger than n50 ()., the transcriptome assembly was evaluated by rnaquast 1.4.0, with default parameters supplying the reference genome sequences and genome annotation of the burmese python (genbank assembly accession: gca_000186305.2)., busco_v2 (busco, […]

rnaQUAST in publications

 (2)
PMCID: 5597892
PMID: 28873961
DOI: 10.1093/gigascience/gix057

[…] it with the burmese python reference genome (genbank assembly accession: gca_000186305.2) and corresponding gene set in the national center for biotechnology information (ncbi) database using rnaquast v. 1.4.0 []. the transcriptome assembly had 34 423 transcripts in total; 34 040 (98%) of these transcripts had at least 1 significant alignment to the reference genome, and 31 102 (91%) […]

PMCID: 5607918
PMID: 28518075
DOI: 10.3791/55009

[…] store (folder 3_assembly) to minimize potential confusion. note: output counts tables for differential gene expression analysis into a folder (4_differential_expression)., assess the assembly using rnaquast (figure 4). move the trinity output files into the folder "3_assembly" in the de and label the folder "a_trinity_de_novo_assembly." give each transcriptome that was assembled a subfolder […]

rnaQUAST institution(s)
Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia; Research and Development Department, EMC, St. Petersburg, Russia
rnaQUAST funding source(s)
This work was supported by EMC Research and Development Department and St. Petersburg State University [grant number 15.61.951.2015].

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