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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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Versioning


No version available

Documentation


Maintainer


  • person_outline Curtis Huttenhower

KneadData citations

 (5)
library_books

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

2017
Genome Med
PMCID: 5704459
PMID: 29183332
DOI: 10.1186/s13073-017-0490-5

[…] 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 the […]

call_split

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

2017
mSystems
PMCID: 5547758
PMID: 28808691
DOI: 10.1128/mSystems.00047-17
call_split See protocol

[…] truction 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). Mouse reads […]

call_split

Multi omics Analysis of Periodontal Pocket Microbial Communities Pre and Posttreatment

2017
mSystems
PMCID: 5513737
PMID: 28744486
DOI: 10.1128/mSystems.00016-17
call_split See protocol

[…] 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 from the same subgingi […]

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

[…] tgun 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 (http://www.ncb […]

library_books

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

2016
mSystems
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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