Microbiome Helper protocols

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Microbiome Helper specifications

Information


Unique identifier OMICS_17830
Name Microbiome Helper
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, Python, R
Computer skills Advanced
Stability Stable
Requirements
FASTQC, PEAR, GNU Parallel, Bowtie2, Human pre-indexed database, DIAMOND, MetaPhlAn2, HUMAnN, FASTX toolkit, BBMap, VSEARCH, QIIME, SortMeRNA, SUMACLUST, PICRUSt, STAMP, 16S chimera, 8S chimera, ITS2 chimera, Eukaryotic OUT, ITS2 OUT
Maintained Yes

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Publication for Microbiome Helper

Microbiome Helper in pipelines

 (2)
2018
PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] the pooled samples were run on an illumina miseq using pe 300 + 300 bp v3 chemistry at the integrated microbiome resource (dalhousie university, halifax, nova scotia)., we followed the microbiome helper standard operating procedure [] to process the 16s rrna gene data. two cd samples (s34 and s38) were excluded from this pipeline due to low dna quality and repeated sequencing […]

2018
PMCID: 5861609
PMID: 29581730
DOI: 10.1186/s13099-018-0239-8

[…] by following the guidelines provided by illumina (san diego, usa; part #15044223, rev. b). the amplified 16s rdna fragments were then sequenced using the illumina miseq platform by using the microbiome helper workflow []. raw sequences were analyzed with qiime (quantitative insight into microbial ecology) and fastqc (v0.11.5) coupled with pear (v0.9.10) was used to evaluate raw reads, […]


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Microbiome Helper in publications

 (6)
PMCID: 5861609
PMID: 29581730
DOI: 10.1186/s13099-018-0239-8

[…] by following the guidelines provided by illumina (san diego, usa; part #15044223, rev. b). the amplified 16s rdna fragments were then sequenced using the illumina miseq platform by using the microbiome helper workflow []. raw sequences were analyzed with qiime (quantitative insight into microbial ecology) and fastqc (v0.11.5) coupled with pear (v0.9.10) was used to evaluate raw reads, […]

PMCID: 5769311
PMID: 29335008
DOI: 10.1186/s40168-018-0398-3

[…] the pooled samples were run on an illumina miseq using pe 300 + 300 bp v3 chemistry at the integrated microbiome resource (dalhousie university, halifax, nova scotia)., we followed the microbiome helper standard operating procedure [] to process the 16s rrna gene data. two cd samples (s34 and s38) were excluded from this pipeline due to low dna quality and repeated sequencing […]

PMCID: 5744928
PMID: 29281673
DOI: 10.1371/journal.pone.0189404

[…] libraries were then pooled and sequenced in a portion of a 300+300 bp pair-end miseq run (illumina 600-cycle v3 kit)., analysis of 16s rrna sequence data was performed as previously described using microbiome helper []. samples from each of the 21 mammals were sequenced only once, with exceptions in the beaver, porcupine, arctic wolf and coyote which were sequenced in biological triplicate. raw […]

PMCID: 5701250
PMID: 29176587
DOI: 10.1038/s41598-017-16560-6

[…] t-test. predicted contribution of each key bacterial species to k01207 and k01443 counts were computed using the script metagenome_contributions.py in picrust and visualized with an rscript in microbiome helper., cecal digesta samples (each about 5 ml) after dilution with oxalic acid (1:1, v/v), were subjected to short chain fatty acids (scfa) analysis by gas chromatography […]

PMCID: 5566786
PMID: 28845459
DOI: 10.1128/mSystems.00006-17

[…] rrna gene amplification, paired-end 300-bp plus 300-bp v3 sequencing was performed for all samples on the illumina miseq., analysis of sequencing data was done on a linux virtual machine, using the microbiome helper workflow, specific to 16s rrna gene analysis, obtained from github (https://github.com/mlangill/microbiome_helper/wiki/16s-standard-operating-procedure). paired-end reads […]


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Microbiome Helper institution(s)
CGEB-Integrated Microbiome Resource (IMR) and Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
Microbiome Helper funding source(s)
Funded through the Dalhousie University Strategic Research Initiatives Fund.

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