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SneakerNetOutput.md

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SneakerNet Output

SneakerNet creates a subdirectory SneakerNet/ in the input folder. In this document, this subfolder will be referred to as SneakerNet/. This document describes those files.

Files under SneakerNet/

properties.txt

This file records special values from each plugin in the format of plugin name, key, value. Duplicate plugin name and key combinations are allowed; however, the last plugin name and key combination overrides the earlier instances. Therefore for example, a warning from a plugin will be "erased" if the plugin is run again and it records a value describing zero warnings. There are some special keys that are treated differently:

  • table - the relative path to a .tsv file from the main folder that describes a summary table from a plugin, e.g., SneakerNet/forEmail/kraken.tsv. This can also be a csv file.
  • version - the version number of the plugin that was run in the format of simple integers separated by periods, e.g., 2.3.1
  • XX-version - the version number of some software used in this specific plugin
  • warnings - a summary of warnings from the plugin, e.g., 5 samples do not have fastq files. Use "0" for no warnings.
  • errors - a summary of errors from the plugin, e.g., Error reading summary table. Use "0" for no errors.
  • date - date of analysis in YYYY-MM-DD format
  • time - time of analysis in HH:MM:SS format
  • other - other keys are allowed but not not specifically described here, e.g., resfinder_gene_drug_version for the staramr plugin. For other special keys, please see the individual plugin documentation pages.

forEmail/passfail.tsv

This file records sample names and categories on which a given sample can pass or fail. Each value for a category is a simple integer.

  • 1 - This sample failed on this category
  • 0 - This sample passed on this category
  • -1 - It is unknown whether this sample passed. For example, if the taxon is unknown and therefore the coverage is unknown.

Other files under forEmail/

Please see individual plugin documentation pages on other files

Subfolders

There are some special subfolders in SneakerNet/.

forEmail

SneakerNet/forEmail/ is the directory that all email attatchments live. Plugins will create summary files, usually tables, and then they will get attached to the report email.

assemblies

SneakerNet/assemblies is the directory that all genome assemblies and gene predictions live. For each sample, e.g., sample1, there is a subfolder, e.g., SneakerNet/assemblies/sample1. There is at least one .fasta and .gbk file in each sample subfolder. Each file is named after the basic assembly method, e.g., SneakerNet/assemblies/sample1/sample1.skesa.fasta.

kraken

SneakerNet/kraken contains a subfolder for each sample name, e.g., SneakerNet/kraken/sample1. In each sample folder, there are kraken output files, or output files compatible with Kraken output files. These files are:

  • kraken.report - a tab-separated file whose values have optional space padding. Its fields are
    • percent of reads
    • number of reads
    • number of reads specific to this exact taxon
    • rank - one letter representation, e.g., S for species
    • taxid
    • Name for the taxon
  • kraken.taxonomy - a tab-separated file whose values are
    • number of reads specific to this exact taxon
    • taxonomy lineage separated by tabs, starting with root and ending with the genus/species name
  • report.html - the Krona html file for visualization

kraken.out is not always present due to space limitations but would describe the taxonomic classification for each read.

Other

Other plugins can create subfolders. For example, the plugin baseBalance.pl creates a subfolder SneakerNet/baseBalance. Please see individual plugin documentation pages for more information.