New Features
Dynamic Top size
The ability for the top size in metagenomic analysis to be dynamically set to the size of the database has been added, it is now the default behaviour.
Alternative Viral Database locations
A new option --alt-viral-db allows specifying a path anywhere on the file system for the viral database to use
Viral Database Metadata
A new option --viral-db-metadata can be used to provided a file which maps accession numbers in the viral database to a label for a viral grouping. These viral groups will be used with the --run-all-v-alig command. This allows the user to specify different viral groups such as splitting A species into subgroups or merging very similar species together.
TRACESPipe does not support altering databases specified with this option.
Minimum Similarity Length Filter
A new option --min-similarity-len can be used to filter which metagenomic hits are good enough to proceed with alignment and consensus calling. Conceptually this generously interprets the FALCON similarity as a contiguous block of the genome, and requires that block to be at least a particular length. This option is by default set to zero (disabled), but a reasonable value would be the average read length for the input library.
Altered Behaviour
Global sensitive alignment
The --very-sensitive option now affects alignments performed using the --run-specific option. Previously one would need to use --run-extreme to get this behaviour.
More Conservative Depth of coverage calculation
The Depth of coverage calculation has been updated such that supplementary and secondary alignments are no longer counted. This ensures that the bases from a single read are counted only once towards the depth of coverage.
Additionally, depths at any single site are capped at 1000 reads, in an attempt to reduce the influence of highly repetitive regions or regions with similarity to the human genome.
Bug Fixes
- Fixed a bug where reference based consensus sequences may have been truncated if incompatible variants were called.
- Dynamic Top size prevents the presence of a single virus highly represented in the database from masking the presence of other viruses
Tweaks
- The Usage Menu has been reorganized into blocks for easier reading
- Repository Now includes Version Notes
- Default Viral groups now reside in the system files
- Refactoring of some code to reduce redundancy and improve maintainability
- Update to dependency versions