KneadData specifications


Unique identifier OMICS_16929
Name KneadData
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTQ, BAM
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Trimmomatic, Bowtie2, JRE, TRF, Fastqc, SAMTools
Maintained Yes



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  • person_outline Curtis Huttenhower <>

KneadData in publications

PMCID: 5904031
PMID: 29675461
DOI: 10.1016/j.jcmgh.2017.11.014

[…] was based on labchip gx touch ht (perkin elmer, waltham, ma) results. sequencing was performed on hiseq 2500 using chemistry highoutput v4 pe125 (illumina). the paired-end reads were filtered using kneaddata v0.5.1 (, which included quality filtering based on trimmomatic and excluded reads mapping to the human genome. a median number of 3.2 × 107 reads […]

PMCID: 5704459
PMID: 29183332
DOI: 10.1186/s13073-017-0490-5

[…] ibd validation cohort. eighty samples from the human microbiome project (hmp) were used as a healthy validation cohort []., the whole metagenome data were trimmed and human reads were filtered using kneaddata using the default parameters. community composition was calculated with metaphlan2 [] using the default settings. functional and pathway composition was calculated with humann2 [] using […]

PMCID: 5547758
PMID: 28808691
DOI: 10.1128/mSystems.00047-17

[…] of unobserved states) (), and functional modules were reconstructed using humann ()., shotgun metagenomic sequences were first adapter trimmed using cutadapt (). mouse reads were removed using kneaddata (, which also trimmed low-quality base pairs (phred score < 20) and filtered short reads (trimmed length of <70% of original length). […]

PMCID: 5513737
PMID: 28744486
DOI: 10.1128/mSystems.00016-17

[…] text s1, pdf file, 0.2 mb., metagenomes were obtained by shotgun sequencing of a subset of 24 samples, 23 of which produced high-quality data. these data were filtered for human contamination with kneaddata ( in choosing the samples for shotgun metagenomic sequencing, we attempted to sequence as many samples as possible […]

PMCID: 5032049
PMID: 27599587
DOI: 10.1021/acs.est.6b00262

[…] sequencing reads were as follows: 1) concatenated into a single fastq file, 2) filtered for low quality reads and human sequence contaminants using knead v0.3 (, and 3) taxonomically classified and quantified using metaphlan2 (, all sequence data are available in the sequence read archive […]

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