Raw data QC

Metagenomic pair-1 FASTQC report Metagenomic pair-2 FASTQC report Metatranscriptomic pair-1 FASTQC report Metatranscriptomic pair-2 FASTQC report

Preprocessed data QC

Metagenomic pair-1 FASTQC report Metagenomic pair-2 FASTQC report Metagenomic single-end FASTQC report Metatranscriptomic pair-1 FASTQC report Metatranscriptomic pair-2 FASTQC report Metatranscriptomic single-end FASTQC report

Assembly visualization, QC and taxonomic annotation

VizBin + contig length VizBin + GC % MetaQUAST report

In order to perform a human augmented binning of the contigs, please import the following fasta file to

Read mapping visualizations

RPKM density beanplot Coverage density beanplot Depth of coverage density beanplot VizBin + metagenomic coverage VizBin + metatranscriptomic coverage VizBin + metagenomic depth of coverage VizBin + metatranscriptomic depth of coverage

In order to perform a human augmented binning of the contigs, please import the following fasta file to

KEGG Ontology based Functional Krona Chart

Metagenome Metatranscriptome

Visualizations of metatranscriptomic to metagenomic ratio

VizBin + depth of coverage ratio VizBin + RPKM ratio

In order to perform a human augmented binning of the contigs, please import the following fasta file to

Variants

Variant count beanplot Variant density beanplot VizBin + metagenomic variant density VizBin + metatranscriptomic variant density

Statistics

Workflow diagram

The workflow is also available in PDF.

Configuration

IMP has run with the configuration file saved at: config.json.

Log

The log files register all commands that have been run by IMP.

The log are accessible in here IMP steps:

Result files

All results files can be found in the root directory of this report.

Please cite the pre-print article on http://biorxiv.org.

IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
Shaman Narayanasamy†, Yohan Jarosz†, Emilie E.L. Muller, Cédric C. Laczny, Malte Herold1, Anne Kaysen, Anna Heintz-Buschart, Nicolás Pinel, Patrick May, and Paul Wilmes*