image/svg+xml by Harald Gruber-Vodicka, Elmar Pruesse, Brandon Seah

High throughput phylogenetic screening using SSU rRNA gene(s) abundance(s)

Click on report section headers to expand, mouse-over underlined text to see explanations.

Library name:

Graphical Summary

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Read-mapping %identity of reads vs. reference database. Lower %identity hits may indicate presence of divergent taxa not represented in the database.
Insert sizes for read pairs. Distribution should generally be unimodal; more than one peak may indicate contamination from other libraries.
Proportion of reads mapped to SSU rRNA database. Typically < 1% for metagenomes, ca. 20% for metatranscriptomes without rRNA depletion or poly-A selection.
Proportion of reads assembled to full-length sequences. High proportion unassembled suggest either assembly failure or high diversity of organisms with low coverage.
Coverage evenness across eukaryotic 18S rRNA gene model from Barrnap, using Nhmmer from random subsample of mapped reads. This helps to detect contamination from tag sequencing libraries (sharp coverage peaks). For the eukaryotic model it is normal to see one or two regions with low coverage because of variable regions in the 18S rRNA gene that are not present in all organisms.
Coverage evenness across prokaryotic 16S rRNA gene model from Barrnap, using Nhmmer from random subsample of mapped reads. This helps to detect contamination from tag sequencing libraries (sharp coverage peaks).

Tree of full-length assembled sequences (Click to hide)

Full-length assembled SSU rRNA sequences along with closest hits from SILVA database, in an alignment guide tree produced by MAFFT. This tree helps to visualize the relatedness of sequences in library to known relatives. Colored circles have areas proportional to the number of SSU rRNA reads that map to each respective sequence (re-mapping is done separately for SPAdes, EMIRGE, and trusted-contig full-length sequence sets). Click on the toggle switches to turn them on and off. Additional circle representing proportion of SSU rRNA reads that were not assembled is in lower right corner. Long taxonomy strings of reference sequences are truncated, but the full strings are given in the tables below.

Color key: Assembled by SPAdes, Reconstructed by EMIRGE, Extracted from trusted contigs, Closest-matching reference sequence from SILVA database

Interactive treemap of mapping-based taxonomic read classification (Click to hide)

Navigation: Left-click to go down, right-click to go up in taxonomic hierarchy, hover to see counts.

Based on read-mapping hits to reference database, provides an approximate overview of taxonomic composition.

Drawn with Google Visualization API (terms of service)

Input parameters

Input command
Forward read file
Reverse read file
Minimum mapping identity %
Working folder
Database used

Results

Mapping statistics

Input PE-reads
Mapped SSU read pairs
Input SE-reads
Mapped SSU SE-reads
Mapping ratio %
Fraction assembled %
Detected median insert size
Used insert size
Insert size standard deviation

Output files

Taxonomic affiliation of SSU rRNA reads in library

Approximate overview of taxonomic composition of ALL reads, based on mapping hits to SILVA SSU rRNA database using BBmap.

NTUs observed once
NTUs observed twice
NTUs observed three or more times
NTU Chao1 richness estimate

Taxonomy summarized at level . Only displaying taxa with > 3 reads mapped.

Taxon Reads

SSU rRNA assembly-based taxa

Full-length SSU rRNA sequences assembled by SPAdes, matched to SILVA database with Vsearch.

OTU Mapped Cov DB hit Taxonomy % ID Alnlen Evalue

SSU rRNA reconstruction-based taxa

Full-length SSU rRNA seqeunces reconstructed by EMIRGE, matched to SILVA database by Vsearch.

OTU Mapped Ratio DB hit Taxonomy % ID Alnlen Evalue

SSU rRNA from trusted contigs

Full-length SSU rRNA seqeunces extracted from trusted contigs file, matched to SILVA database by Vsearch.

OTU Mapped DB hit Taxonomy % ID Alnlen Evalue

Taxonomic affiliation of unassembled SSU rRNA reads

Approximate overview of taxonomic composition for reads that did NOT assemble into full-length sequences, based on mapping hits to SILVA SSU rRNA database with BBmap.

Taxonomy summarized at level . Only displaying taxa with > 3 reads mapped.

Taxon Reads

Please cite...

Harald R Gruber-Vodicka, Brandon KB Seah, Elmar Pruesse. 2019 (preprint). phyloFlash - Rapid SSU rRNA profiling and targeted assembly from metagenomes. bioRxiv 521922; doi: https://doi.org/10.1101/521922

Cite dependencies when used