SortMeRNA pipeline

SortMeRNA specifications

Information


Unique identifier OMICS_02619
Name SortMeRNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Jenya Kopylov <>

Publication for SortMeRNA

SortMeRNA citations

 (5)
2018
PMCID: 5945926

[…] of quality filtered reads are given in parentheses. the values were calculated in relation to the number of raw reads per sample. the proportions of reads derived from rrna and non-rrna using sortmerna were calculated in relation to the total number of quality filtered reads per sample., reads that aligned to rrna databases were identified and excluded from further analyses […]

2017
PMCID: 5909424

[…] in single-end (se) with a read length of 100 bases on one lane of hiseq2000 machine to obtained around 25 million reads. after adaptor trimming and t- and r-rna removing, using cutadapt57 and sortmerna,58 respectively, small rnas of 24-nt length were selected using prinseq v0.20.4.59 redundant and non-redundant (nr) data sets of 24-nt srnas were then mapped on g19833 genome sequence […]

2017
PMCID: 5582611

[…] were functionally annotated using various databases to obtain a transcriptome profile. all steps are described in further detail in the following paragraphs., we filtered raw fastq reads using sortmerna-v2.1 (kopylova, noé & touzet, 2012) against 8 default rrna databases (silva 16s bacteria, silva 16s archaea, silva 18s eukarya, silva 23s bacteria, silva 23s archaea, silva 28s eukarya, […]

2016
PMCID: 4795696

[…] reads were filtered and trimmed by prinseq-lite using parameters trim_qual_right 30, min_qual_mean 30, min_len 70, trim_tail_right 6, trim_tail_left 6, and rrna sequences were removed using sortmerna 1.99 [8]. digital normalization (maximal coverage 30) and transcript assembly were performed using trinity pipeline (release 2013-02-25, [9])., protein-coding sequences were identified […]

2015
PMCID: 4689417

[…] were eliminated using an in-house perl script and low-quality bases were trimmed with clc ngs cell (clc bio, denmark) with cut-off values q20. finally, rrna sequences were filtered out using sortmerna [29]., de novo assembly was performed using clc ngs cell to construct unigene sets for ‘am’ and ‘ts’. orthologous unigene sets were searched and aligned using nucleotide blast searches. […]

SortMeRNA institution(s)
LIFL, UMR CNRS 8022, Université Lille 1, France

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