Kaiju protocols

Kaiju specifications

Information


Unique identifier OMICS_11856
Name Kaiju
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data HTS reads
Input format FASTQ and FASTA format
Output data Taxonomic classification
Output format TSV
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux, Mac OS
Programming languages C, C++
Parallelization Other
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4
First release date 2016
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Anders Krogh <>

Information


Unique identifier OMICS_11856
Name Kaiju
Interface Web user interface
Restrictions to use None
Input data Nucleotide sequences
Input format FASTA or FASTQ
Output data Taxonomic classification
Output format TSV
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Programming languages C, C++
Computer skills Basic
Version 1.4
First release date 2016
Stability Stable
Source code URL https://codeload.github.com/bioinformatics-centre/kaiju/zip/master
Maintained Yes

Maintainer


  • person_outline Anders Krogh <>

Publication for Kaiju

Kaiju IN pipelines

 (2)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] university of cambridge (cambridge, uk)., raw reads from three individual samples were pre-processed using bbtools (6) and coassembled using metaspades (7). contigs were taxonomically assigned using kaiju (8) and binned on the basis of gc% and differential coverage using concoct (9)., the resulting bins were manually refined to reduce contamination using anvi’o (10); briefly, for each bin, […]

2017
PMCID: 5646401
PMID: 29051248
DOI: 10.1128/genomeA.01104-17

[…] and low-quality reads. the high-quality reads were assembled through clc genomics workbench. prodigal 2.6.3 (5) was used with default parameters to predict genes from the assembled scaffolds. kaiju (6) (a program for sensitive taxonomic classification of high-throughput metagenomic sequencing data) was used for taxonomical analysis of the predicted genes, and functional analysis of genes […]

Kaiju institution(s)
Department of Biology, University of Copenhagen, Copenhagen, Denmark

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