UVP Version 2.7.0

1. Updated command line options to include flags for threading and path to kraken database

2. User has option to edit and use default config file, supply a config file or supply command line opions for threading and kraken database local path

UVP Version 2.6.0

Updated with bioconda functionalities for installation.

Modified file structure and contents to ease installation and accessibility.

Simplified setup and config files.

UVP Version 2.5.1

1. Minor edits in the mutation_loci file to update geneids for erm(37) and Rv3008 upstream loci

2. Modified handling of fastq files that fail QC

3. Included specific language in batch log for isolates with no MTBC lineage SNPs

UVP Version 2.4.1

1. Updated annotation script to handle complementary strand annotation

UVP Version 2.3.1

1. Updated NC_000962.3.gbk file (for SnpEff annotation) to reflect ReSeqTB expert panel agreed gene names and IDs

2. Updated BED type file of H37Rv genome loci

3. Updated annotation interpretation custom script (parse_annotation.py) to customize updated version of ReSeqTB loci of interest list and upstream regions there in.

4. Streamlined UVP to get rid of the resistance loci only annotation

5. Simplified the deleted loci text file to capture only sample IDs, loci coordinates, gene names, gene IDs and variant type.

UVP Version 2.2.1

1. Included custom annotation of 9 additional promoter regions in H37Rv genome

2. Updated mutation_loci.txt to include additional upstream coordinates

UVP Version 2.1.2

1. Streamlined UVP functions

2. Updated QC and Mapping steps

UVP Version 2.1.1

1. Updated Configuration file
2. Renamed pipeline python Scripts

UVP Version 2.1.0

1. Included Configuration file to point to relative file paths

UVP Version 2.0.0

1. Overhauled coverage analysis scripts to incorporate loci across entire genome
2. Incorporated custom annotation of additional 70 promoter regions