SortMeRNA protocols

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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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Maintainer


  • person_outline Jenya Kopylov <>

Publication for SortMeRNA

SortMeRNA in pipelines

 (42)
2018
PMCID: 5753479
PMID: 29298680
DOI: 10.1186/s12864-017-4382-2

[…] 95 bp for p. latipinna and p. mexicana. the average phred quality of the reads was about 36 (table ). before the assembly, the read pairs which presented potential rrna fragments were removed with sortmerna (0.49% for p. formosa | 0.85% for p. latipinna | 0.89% for p. mexicana). the processed reads for all three species can be obtained from the sequence read archive (sra) at the national […]

2018
PMCID: 5766104
PMID: 29329292
DOI: 10.1371/journal.pone.0189898

[…] were removed with trimmomatic 0.33 [] at the q20 level. reads containing ribosomal rna (rrna) sequences were erased from the dataset to avoid mis-annotation of rrnas as putative proteins [] using sortmerna version 2.0 []. the kraken taxonomic sequence classification system version 0.10.5 [] was applied to filter out prokaryotic sequences. those reads belong potentially to microorganisms […]

2018
PMCID: 5797369
PMID: 29434651
DOI: 10.1186/s13007-018-0275-x

[…] with a multiplexing rate of 4 libraries/lane., the raw data (fastq) were trimmed for phred quality score > 20, read length > 30 bases, and the ribosome sequences were removed with tool sortmerna []. the mapper bowtie version 2 [] was used to align reads against the a. thaliana transcriptome (with ‘local’ option and other default parameters). the 33602 annotated genes were extracted […]

2018
PMCID: 5852087
PMID: 29540736
DOI: 10.1038/s41598-018-22617-x

[…] protocol. single read sequencing was done with an illumina hiseq. 2500 (gatc-biotech, konstanz, germany) generating reads between 6.02 to 46.4 m per sample. the read length was 150 bp., sortmerna v1.9 was used to remove rrna reads. trueseq adapters were trimmed with cutadapt v1.2.1 with the –b settings. quality trimming was performed with prinseq lite v0.20.2, with a minimum […]

2018
PMCID: 5864233
PMID: 29476140
DOI: 10.1038/s41396-018-0074-4

[…] 2.4 (parameters: -f -6 -t 0.32, quality cutoff of 0.32 []), and quality-filtered using sickle v. 1.33 (length threshold set to 50 []). reads mapping to ribosomal rna (rrna) were then removed using sortmerna v. 2.140 to arrive at the final set of joined non-rrna reads. these reads were mapped to the non-redundant set of genes in the station aloha gene catalog [] using last, and a 95% id cutoff […]


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SortMeRNA in publications

 (116)
PMCID: 5948854
PMID: 29753320
DOI: 10.1186/s12933-018-0713-0

[…] 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 […]

PMCID: 5945926
PMID: 29780371
DOI: 10.3389/fmicb.2018.00859

[…] non-suppressive samples., 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., ). […]

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

[…] 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 […]

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

[…] 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+) […]

PMCID: 5947290
PMID: 29468803
DOI: 10.1111/1462-2920.14077

[…] (i.e., relative to the geometric mean count of each gene per draft genome)., quality‐controlled (see above) metagenomic (paired‐end forward reads) and metatranscriptomic reads were sorted using sortmerna (v2.1; kopylova et al., 2012) into collections of reads corresponding to the bacterial 23s and 16s rrna, the archaeal 23s and 16s rrna, the eukaryotic 28s and 18s rrna, the 5s rrna […]


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

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