INNUca specifications


Unique identifier OMICS_32459
Name INNUca
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, Perl, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 4.0
Stability Stable
Java JDK, Kraken, mlst, ReMatCh, gzip
Maintained Yes




No version available


  • person_outline Miguel Machado

Additional information

INNUca citations


Origin, evolution, and distribution of the molecular machinery for biosynthesis of sialylated lipooligosaccharide structures in Campylobacter coli

Sci Rep
PMCID: 5813019
PMID: 29445215
DOI: 10.1038/s41598-018-21438-2

[…] For a set of C. coli strains of interest, raw sequencing data were retrieved from ENA with getSeqENA ( Then, the paired-end raw reads were assembled using the INNUca pipeline (, which consists of several modules and QA/QC steps. In brief, INNUca starts by calculating if the sample raw data fulfill the expected coverage […]


Whole genome sequencing for typing and characterisation of Listeria monocytogenes isolated in a rabbit meat processing plant

PMCID: 5641673
PMID: 29071246
DOI: 10.4081/ijfs.2017.6879
call_split See protocol

[…] . The whole genome of selected 34 L. monocytogenes isolates was sequenced using Illumina MiSeq platform (TrueSeq library, paired-end reads). Reads were quality checked and de novo assembled using the INNUca pipeline ( /INNUENDOCON/INNUca).Briefly, INNUca calculates if the sample raw data fulfill the expected coverage (minimum default 15X). Then, after a read quality analysis usin […]

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