Releases: plantinformatics/brioche
Releases · plantinformatics/brioche
Brioche v2.0.0
Brioche v2.0.0
Release Notes
New features
- Users can now include supplementary information files (priors files) to assist with Brioche determining the optimal mapping location for individual markers.
- Users can now run Brioche iteratively to extract insilico genotypes from one or more reference genomes for a given marker dataset.
- Brioche can now anchor three types of sequencing data against a reference genome. Genotype matrix data, VCF files, DArT sequencing reports. Brioche will take any of these three and output the results as a standardised VCF file mapped against the user chosen reference genome.
- Brioche can now track tri+ allelic states when anchoring against genomes.
- Brioche can now track the presence of NULL alleles in both sequenced samples during anchoring and in reference genomes markers are mapped against.
- Brioche can now track unmapped markers in VCF files to preserve genotype data between reference anchoring.
- Brioche can now track the presence and number of local duplications of marker squences within a user given upstream/downstream variable range.
- Brioche now comes multiple bash scripts to assist with the specific usecases e.g., identifying optimal mapping conditions, mapping 1,000,000+ markers, anchoring any dataset using pre-made brioche mapping files.
- Brioche now has a detailed user guide describing how to set up and run the program as well as highlighting specific usecases for the program.
- Brioche now has specifically demarcated results files for each individual filtering step run allowing for transparency of when/where/how individual markers were mapped/not mapped
- Brioche now produces a summary html report with each run.
- Brioche now tracks all metadata around settings used and brioche version, and populations results files (including VCFs) with this information.
- Brioche now contains scripts to help generate a Brioche input file from a VCF file or a DArT sequencing report (1 row per marker).
Improvements
- Brioche now splits data into user specified sized chunks for blastn and executes each chunk as a separate process reducing time and memory required to run Brioche.
- Input files are now sanitised for non unix formats and for excess newline spacing at the end of files
- Example files are now provided for every input file type to assist the user.
