Protocols

INNUca specifications

Information


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
Requirements
Java JDK, Kraken, mlst, ReMatCh, gzip
Maintained Yes

Download


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Versioning


No version available

Maintainer


  • person_outline Miguel Machado

Additional information


http://www.innuendoweb.org/news-and-events/innuca-oursoftwarepipelineforautomaticqaqcmeasuresoffastqreads

INNUca citations

 (2)
library_books

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

2018
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 (https://github.com/B-UMMI/getSeqENA). Then, the paired-end raw reads were assembled using the INNUca pipeline (https://github.com/INNUENDOCON/INNUca), which consists of several modules and QA/QC steps. In brief, INNUca starts by calculating if the sample raw data fulfill the expected coverage […]

call_split

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

2017
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 (https://github.com /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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