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KneadData specifications

Information


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
Requirements
Trimmomatic, Bowtie2, JRE, TRF, Fastqc, SAMTools
Maintained Yes

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Documentation


Maintainer


  • person_outline Curtis Huttenhower <>

KneadData citations

 (6)
library_books

Antibiotic Treatment Leads to Fecal Escherichia coli and Coliphage Expansion in Severely Malnourished Diarrhea Patients

2017
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 (https://bitbucket.org/biobakery/kneaddata), which included quality filtering based on trimmomatic and excluded reads mapping to the human genome. a median number of 3.2 × 107 reads […]

library_books

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

2017
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 […]

library_books

Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice

2017
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 (http://huttenhower.sph.harvard.edu/kneaddata), which also trimmed low-quality base pairs (phred score < 20) and filtered short reads (trimmed length of <70% of original length). […]

library_books

Multi omics Analysis of Periodontal Pocket Microbial Communities Pre and Posttreatment

2017
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 (https://bitbucket.org/biobakery/kneaddata/wiki/home). in choosing the samples for shotgun metagenomic sequencing, we attempted to sequence as many samples as possible […]

library_books

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome

2016
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 (http://huttenhower.sph.harvard.edu/kneaddata), and 3) taxonomically classified and quantified using metaphlan2 (http://huttenhower.sph.harvard.edu/metaphlan2)., all sequence data are available in the sequence read archive […]

library_books

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

2016
PMCID: 5069760
PMID: 27822528
DOI: 10.1128/mSystems.00018-16

[…] were constructed using the illumina nextera xt method and sequenced on an illumina hiseq 2000 platform with 100-bp paired-end (pe) reads. the sequencing depth was 16.7 × 106 pe reads per sample. the kneaddata v0.3 pipeline (http://huttenhower.sph.harvard.edu/kneaddata) was used to remove low-quality reads and human host sequences. further details can be found in  in the supplemental material., […]


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