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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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Versioning


No version available

Maintainer


  • person_outline Jenya Kopylov

Publication for SortMeRNA

SortMeRNA citations

 (155)
library_books

Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart

2018
PMCID: 5948854
PMID: 29753320
DOI: 10.1186/s12933-018-0713-0

[…] EMBL Heidelberg, Germany). The number of reads (minimum, 32 million; maximum, 73 million) was filtered out by TrimmomaticPE version 0.36 []. Ribosomal RNA and mitochondrial reads were filtered out by Sortmerna (version 2.1b []) using default parameters. RNAseq reads were mapped to the mouse genome using STAR (version 2.5.2b []) version GRCm38 primary assembly and annotation version M8. Count table […]

library_books

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non suppressive Soils for Rhizoctonia solani AG8

2018
Front Microbiol
PMCID: 5945926
PMID: 29780371
DOI: 10.3389/fmicb.2018.00859

[…] Despite mRNA enrichment, the remaining rRNA sequences were removed prior to BLASTX analyses of the filtered sequence reads. Ribosomal RNA removal was performed using the SortMeRNA software with the eight default rRNA databases included in the software package, covering the small (16S/18S), large (23S/28S), and 5/5.8S ribosomal subunit (Kopylova et al., ). The non-rRNA […]

library_books

Larval transcriptomic response to host plants in two related phytophagous lepidopteran species: implications for host specialization and species divergence

2018
BMC Genomics
PMCID: 5907310
PMID: 29669517
DOI: 10.1186/s12864-018-4589-x

[…] quality control and trimming with Trimmomatic v0.25, to remove Illumina sequencing adapters and low-quality reads []. After quality control, the ribosomal and bacterial contaminants were removed with SortMeRNA v2.0 [], which takes as input the files containing all high-quality reads and multiple rRNA database files (16S and 23S for bacteria and archae and 18S and 28S for eukarya) to sort apart in […]

library_books

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

2018
mSystems
PMCID: 5904434
PMID: 29719869
DOI: 10.1128/mSystems.00021-18

[…] bad gut health (assessed via mannitol-lactulose tests). The same demultiplexed raw reads were rarefied to 11,000 reads per sample for “closed-reference” picking via QIIME1’s script parallel_pick_otus_sortmerna.py with default parameters and were rarefied to 12,500 reads per sample for “open-reference” picking (using QIIME1’s script pick_open_reference_otus.py with default settings) and to 7,500 re […]

library_books

A new way of producing pediocin in Pediococcus acidilactici through intracellular stimulation by internalized inulin nanoparticles

2018
Sci Rep
PMCID: 5897564
PMID: 29650991
DOI: 10.1038/s41598-018-24227-z

[…] equenced using HiSeq. 2500 (Illumina, CA, USA) for 100-bp paired-end reads. Adapter sequences of the reads were trimmed with Cutadapt1.10, and ribosomal RNA sequences were removed in silico using the SortMeRNA program. The sequence reads were quality-filtered using in-house Perl scripts. In brief, when 95% of the nucleotide bases in a read were given a quality score over 31 (Illumina 1.8+) and the […]

library_books

Ginseng Genome Database: an open access platform for genomics of Panax ginseng

2018
BMC Plant Biol
PMCID: 5898050
PMID: 29649979
DOI: 10.1186/s12870-018-1282-9

[…] nst the available bacterial genomes using BWA []. After pre-processing, the duplicated reads were filtered out using FastUniq []. The third step is the removal of the ribosomal RNA (rRNA) reads using SortMeRNA []. Finally, the low-quality reads were removed using NGS QC Toolkit []. The high-quality RNA-Seq reads were used for de novo assembly by Trinity [] and reference-guided assembly by HISAT & […]

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

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