ERNE pipeline

ERNE specifications


Unique identifier OMICS_00662
Alternative name Extended Randomized Numerical alignEr
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes


  • ERNE-BS5



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Publication for Extended Randomized Numerical alignEr

ERNE IN pipelines

PMCID: 5448768
PMID: 28558066
DOI: 10.1371/journal.pone.0178119

[…] mode in one run on the illumina hiseq™-2000 platform, generating up to 30 m reads of 100 bp per sample. sequences derived from contaminating microorganisms were removed from the raw data using erne-filter. adaptor trimming, quality control and de novo assembly were performed using clc genomics workbench ( adapters were trimmed using mismatch costs of 2 and a gap […]

PMCID: 5639751
PMID: 29025411
DOI: 10.1186/s12870-017-1108-1

[…] adapter clipping using cutadapt 1.2.1 [94] and then trimmed on quality scores and filtered from rrna contaminant reads (rrna reference sequences were retrieved from with erne-filter 1.2 [95]. the resulting high quality reads (additional file 1) were mapped to the maize b73 reference genome (refgen zmb73 assembly agpv3 and zea_mays.agpv3.20.gtf transcript annotation) […]

PMCID: 4962059
PMID: 27461139
DOI: 10.1038/srep30446

[…] in supplementary figure s1, the sequenced reads were first processed for adapter clipping using cutadapt 1.2.126 and then trimmed on quality scores and filtered from rrna contaminant reads with erne-filter 1.227 using ribosomal rna sequences retrieved from the “silva ribosomal rna gene database project” ( as contaminant reference. the resulting high quality reads […]

ERNE institution(s)
Department of Mathematics and Computer Science, University of Udine, Udine, Italy

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