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Microbiome Analysis Report

Analysis run name:
 V4-emp
Date generated:Tue Dec 11 14:44:27 CST 2018
Samples:46
Library type:Paired-end
Fastq folder:/panfs/roc/groups/8/umgc-staff/jgarbe/pipelines/metagenomic/V4-emp
Commandline:/panfs/roc/groups/3/umii/public/gopher-pipelines/dev/bin/metagenomics-pipeline.pl –subsample 1000 –emp –fastqfolder V4-emp –scratchfolder /panfs/roc/scratch/pipelines/metagenomics/V4-emp-test –threadspersample 16 –bowtie2index /panfs/roc/rissdb/genomes/Escherichia_coli/eschColi_K12/bowtie2/eschColi_K12
Program versions:
 programversions.txt
Sample metrics:metrics.html metrics.txt

Quality Plots

Resources/qualityplot.png Resources/metricspercentplot.png Resources/metricsplot.png Resources/fragmentlengths.png

The chart above uses boxplots to show the distribution of stitched fragment lengths before the removal of chimeric and contaminating host sequences. The distribution is often very small resulting in flattened boxes (in green) with a few outliers (black dots).

Resources/filteredfragmentlengths.png

The chart above uses boxplots to show the distribution of stitched fragment lengths after the removal of chimeric and contaminating host sequences (when host is specified). The distribution is often very small resulting in flattened boxes (in green) with a few outliers (black dots).

OTU Plots

Resources/taxoncounts.png
OTU Heatmap:otu-heatmap.png
Taxa Summary Area Charts:
 area_charts.html
Taxa Summary Bar charts:
 bar_charts.html

Diversity Plots

Alpha Rarefaction Plots:
 rarefactionplots.html
Beta Diversity - unweighted unifrac pcoa:
 index.html
Beta Diversity - weighted unifrac pcoa:
 index.html

Data

The primary output of this analysis pipeline is the quality-control information shown in this document, as well as the following data:

Intermediate and temporary files

While the primary output files contain the most important results of the analysis, some users may be interested in the intermediate files generated during the analysis of the experiment. Full output from this analysis is available for a limited time on the MSI filesystem at /panfs/roc/scratch/pipelines/metagenomics/V4-emp-test. This data will be deleted on Thu Jan 10 2019. Copy the full output to your home directory:

cp -r /panfs/roc/scratch/pipelines/metagenomics/V4-emp-test ~/

Copy an individual folder to your home directory:

cp -rL /panfs/roc/scratch/pipelines/metagenomics/V4-emp-test/alpha ~/

Contents of /panfs/roc/scratch/pipelines/metagenomics/V4-emp-test:

adapttrim:Fastq files for all samples with sequencing adapters removed
rarefaction:Output from Qiime’s alpha_rarefaction.py workflow script
beta:Output from Qiime’s beta_diversity.py script
alpha:Output from Qiime’s alpha_diversity.py script
chimeras:Output from Qiime’s identify_chimeric_seqs.py script
fasta:Fasta files for all samples
fasta-subsampled:
 Fasta files for all samples, subsampled (if subsampling of filtered reads was enabled)
fastq:Symlinks (shortcuts) to fastq files for all samples
fastq-subsampled:
 Fastq files for all samples, subsampled (if subsampling was enabled
logs:
otuplot:Output from Qiime’s make_otu_heatmap_html.py, make_otu_network.py, and summarize_taxa_through_plots.py scripts
output:Summary plots, html report, otu_table.biom, rep_set.tre
petrim:Fasta files for each sample with amplicon adapters removed (paired-end datasets only)
pickotus:Output from Qiime’s pick_open_reference_otus.py workflow script
setrim:Fasta files for each sample with amplicon adapters removed (single-end datasets only)
sphinx:Temporary files used to create html report

Methods

The metagenomics pipeline implements the Qiime 1.9.1 open-reference OTU calling method with the greengenes 16s reference or UNITE ITS reference. Sequencing adapter sequences are trimmed from the 3’ ends of reads using Trimmomatic. PandaSeq is used to removed primer sequences from the beginning of reads and to stitch the overlapping paired reads together. Reads without primer sequences and reads that cannot be stitched together are discarded. Stitched reads whose length are outside the expected length of the targeted variable region are discarded. Chimeric sequences are identified and removed using the identify_chimeric_seqs Qiime function with the usearch61 method. Contaminating host sequences are identified and discarded by aligning stitched reads to the HOST reference genome using BWA/BOWTIE2 [if a bwa or bowtie2 index was provided to the pipeline]. An OTU table is constructed using the Qiime open-reference OTU picking workflow using the greengenes reference database. OTU table summary plots and alpha and beta diversity metrics are generated using Qiime workflows.

Acknowledgments

The report is provided by the University of Minnesota Informatics Institute. UMII is an institute of the Office of the Vice President for Research. The automated analysis pipeline was developed with funds from the University of Minnesota Informatics Institute in collaboration with the University of Minnesota Genomics Center and the RIS group at the University of Minnesota Supercomputing Institute.

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