SortMeRNA protocols

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 IN pipelines

 (11)
2018
PMCID: 5835687
PMID: 29541079
DOI: 10.3389/fpls.2018.00149

[…] the random tagged prime rna-seq data was first analyzed with the common ngs (next generation sequencing) analysis tools: first, the entire rrna database provided by the tool was analyzed with sortmerna (v 2.1; kopylova et al., 2012). from the remaining reads, the low-quality reads (below 20 quality score) were trimmed using trimmomatic (v 0.36) (bolger et al., 2014) and the parameters […]

2017
PMCID: 5281551
PMID: 28197133
DOI: 10.3389/fmicb.2017.00067

[…] table s8). paired-end reads were merged using the fastq-join program 4 with default parameters. ribosomal rna (5s, 5.8s, 16s, 18s, 23s, and 28s) were identified from merged reads using sortmerna 2.0 (kopylova et al., 2012) (rrid:scr_014402) and picked from rna-seq data. non-rrna sequences, theoretically corresponding to putative mrna, were assembled de novo using trinity […]

2017
PMCID: 5364173
PMID: 28392779
DOI: 10.3389/fmicb.2017.00442

[…] 2 version 2.2.4 (langmead and salzberg, 2012) with one mismatch in the seed and multiple hits reporting enabled. ribosomal rna was removed from metatranscriptomic datasets prior to mapping employing sortmerna version 2.0 (kopylova et al., 2012). the number of unique sequences per gene was calculated as described previously (wemheuer et al., 2015). in addition, coverage was determined […]

2017
PMCID: 5483018
PMID: 28483981
DOI: 10.1242/bio.023739

[…] hiseq 2500 platform with 50 bp paired-end mode and sequencing depth of approximately 36 million reads per sample., data analysis was performed in-house. ribosomal rna reads were filtered out by sortmerna version 2.0 (kopylova et al., 2012) and low quality reads and adaptors were filtered out by trimmomatic version 0.35 for paired end reads (bolger et al., 2014) using parameters: […]

2017
PMCID: 5540255
PMID: 28782034
DOI: 10.1126/sciadv.1603229

[…] than 50 base pairs (bp), contained ambiguous (n) bases, and were of low quality (below 20) were discarded using sickle (https://github.com/najoshi/sickle). rrna reads were further screened using sortmerna (http://bioinfo.lifl.fr/rna/sortmerna/). the trinity de novo assembly pipeline was used to assemble the high-quality paired-end mrna reads (71, 72). resulting sequences were filtered […]

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

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