Output¶
Full listing of expected output files¶
MetAMOS generates an interactive web page once a run successfully completes:
http://www.cbcb.umd.edu/~sergek/imetamos/gageb/Postprocess/out/html/summary.html
This includes summary statistics and taxonomic information based on Krona [1]. The easiest way to interact with the results is through the web interface. The web interface has been tested in several browsers. The currently known issues are:
| Browser | Version | Issues |
|---|---|---|
| Chrome | 33.0.1750.152 | None |
| Safari | 6.1.2 | None |
| Firefox | 28 | QUAST reports do not show for Validate |
| IE | 9 | Not Tested |
The Postprocess/out directory contains the results of the analysis. By default, metAMOS uses the prefix “proba” (Galician for test). Thus, files will have the name “proba”.*.
abundance.krona.html¶
Krona [1] plot of abundances using the tool selected for abundance (MetaPhyler [2] by default)
annotate.krona.html¶
Krona [1] plot of abundances using the tool selected for classification (Kraken [3] by default)
asm.scores¶
Validation scores for each assembly/kmer combination run. Header contains information on scores generated
best.asm¶
The name of the assembly/kmer combination that was selected as the best
<taxonomy>.classified¶
Subdirectory containing each level of the selected taxonomy (class by default) and the contigs/reads/orfs belonging to each
<taxonomy>.original.annots¶
Tab-delimited taxonomic level assignments for each contig/unassembled read. Class IDs correspond to NCBI taxonomy IDs.
<taxonomy>.original.reads.annots¶
Tab-delimited taxonomic level assignments as above, where contigs are replaced with their constituent sequences.
<taxonomy>.propagated.annots¶
Tab-delimited file as above after assembly graph-based propagation of assignments to contigs.
<taxonomy>.propagated.reads.annots¶
Tab-delimited file as above after propagation and having contigs replaced with their constituent reads.
html (directory)¶
HTML output from the pipeline. summary.html contains an interactive results view.
proba.bnk¶
AMOS bank format of the assembly that can be visualized using Hawkeye.
proba.classify.txt¶
The raw output of the abundances using the tool selected for abundance estimations (MetaPhyler [2] by default)
proba.ctg.cnt¶
The number of sequences mapped to each assembly contig
proba.ctg.cvg¶
The coverage of each assembly contig
proba.ctg.fa¶
The assembled contigs
proba.hits¶
The raw output of the contig/unassembled reads classifications using the selected tool (Kraken [3]) by default.
proba.lib1.contig.reads¶
The per-library assignment of sequences to contigs
proba.lib1.unaligned.fasta¶
The per-library unassembled sequences
proba.scf.fa¶
The assembled scaffolds
proba.motifs.fa¶
The motifs within scaffolds identified by Bambus 2
proba.orf.faa¶
The protein sequences of identified open reading frames (ORFs) in the assembly and unassembled reads
proba.orf.fna¶
The fasta sequences of identified open reading frames (ORFs) in the assembly and unassembled reads
proba.scf.orf.faa¶
The protein sequences of identified open reading frames (ORFs) in the scaffolds
proba.scf.orf.fna¶
The protein sequences of identified open reading frames (ORFs) in the scaffolds
ref.fasta¶
The recruited reference genome used for validation (iMetAMOS only)
ref.name¶
The name of the recruited reference genome (iMetAMOS only)
Additional details for each step are available under <STEP NAME>/out. This includes the raw output (as well as any intermediate files) of any tools run during that step. For example, Annotate/out/proba.prokka includes the full Prokka annotation output. Assemble/out/abyss*/ contains the intermediate files output by ABySS. Additionally, since MetAMOS stores all of its results in an AMOS bank, the assemblies can be visualized with Hawkeye.
[1] Ondov BD, Bergman NH, Phillippy AM.. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385. PMID: 21961884
[2] Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.
[3] Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.