Output

Output file descriptions

Within your experiment folder, you will find the following files and folders. This list is not exhaustive and some of the persistent files created by Castanet are not human-readable.

1. consensus_data: Castanet will attempt to generate a consensus sequence for each organism with reads mapped to it, ONLY IF reads have coverage, depth and map quality that exceed the thresholds the user specifies (see "Parameter descriptions" section): these are 30%, 10 and 1.0, respectively, by default. When a consensus has been generated, it will be in a sub-folder whose name is that of the organism.
   1. {name}_remapped_consensus_sequence.fasta: your final consensus sequence.
   2. {name}_consensus_coverage.png: plot of per-position coverage across your consensus.
   3. {name}_target_consensus_alignment.png: alignment plot of your per-target subconsensues with their respective mapping reference sequences.
2. Depth_output: This folder will contain graphs showing per-position read depth, for both total and deduplicated (unique) reads, for each organism with a significant number of reads.
3. {ExpName}_depth.csv: This spreadsheet contains the main numerical output from Castanet. Please refer to the supplementary information spreadsheet from our article for a detailled description of each statistic.
4. {ExpName}_read_distributions.png: Pie chart showing distribution of reads between each organism.