lusSTR version 0.10

• Added GUI using streamlit Python package (#74)
• Added custom sequence ranges for PowerSeq data to accommodate the ISFG recommendations (#75)
• Added the creation of log files and record of configuration settings for each lusSTR run (#76)
• Updated how Kintelligence SNP data was outputted to accommodate use in MixDeR (#73)

lusSTR version 0.9

• Added GeneMarker files as acceptable input for PowerSeq data (#67)
• Enhanced the marker plots with coloring by allele type, adding AT line, and creating third set of marker plots containing only the Typed alleles (#69)
• Further developed processing PowerSeq data by accommodating the newest STRait Razor STR config file, PowerSeqv2.31.config, (#68) and accounting for known indels within the PowerSeq flanking sequences of several STR markers (#70)

lusSTR version 0.8

• Create output files for MPSproto using the sequence bracketed form (#64)
• Remove pkg_resources package due to upcoming deprecation (#65)
• Update Python and Matplotlib versions (#66)

lusSTR version 0.7

• Added LUS+ as possible data type for applying filters and creating files for use in EuroForMix (#57)
• Split Kintelligence SNP data into 10 bins ordered by marker read counts for use in EuroForMix (#58)
• Added ability to accommodate Kintelligence data analyzed using UAS version 2.5 (#59 and #60)
  o Different file format
  o Differing SNP rsIDs
  o All SNPs reported on forward strand
• Create two sets of marker plots for STR data to mimic an STR electropherogram (#61)
  o The y-axis (read counts) scaled for each individual marker
  o The y-axis (read counts) scaled equally for all markers to the marker with the highest read counts
• Small bug fix in applying the detection threshold (#56)

lusSTR version 0.6.4

Updated MANIFEST

lusSTR version 0.6.3

Fixed bug in the creation of SNP config file (set default for sample input as cwd) and bug in MANIFEST and setup.py (#55).

lusSTR version 0.6.2

Fixed fixed bug in setup.py and formatting problem in README.

lusSTR version 0.6.1

Updated README (#54)

lusSTR version 0.6

• Small bugs within the conversion of FGA, D13 and D21 were fixed (#46, #47 and #48)
• Filtering using various thresholds (detection, analytical, stutter and same size) can now be applied using either the CE allele (#49) or the bracketed sequence form (#51).
• Create output files for STRmix (using CE allele or bracketed sequence form) and EuroForMix (CE allele only) (#49)
  • Can be formatted as either evidence or reference files
• Workflows for STRs and SNPs are now organized using Snakemake (#52 and #53)
  • A config file is now required for running lusSTR (created using the command lusstr config)
  • All steps of the workflow can be run in a single command (lusstr strs all or lusstr snps all)
• The SNP workflow can now process SNPs derived from the Kintelligence assay (#53)
• The SNP workflow can now create evidence and reference files for input into EuroForMix (#53)
• Minor changes to headers and code style (#50)

lusSTR version 0.5

• lusSTR can now process ForenSeq SNP data either from a UAS Sample Details and Phenotype Reports or from STRait Razor output (#40).
  • Reports the called allele(s) for each SNP as the strand reported by the UAS and the positive strand.
  • Allows for the option to select specific types of SNPs (identity, ancestry/phenotype or all).
• Fixed bug with combining reads for identical UAS region sequences for X&Y STR loci (#42).
• Removes Amelogenin sequences from files in annotate command (prevents errors when using files that were not run through the format command; #42).
• Adds ability to input an individual STRait Razor output file into the format command (#42).
• lusSTR now has the option to separate the final output file into individual files for each sample ID (using the --separate flag; #43)
  • Available for both STRs and SNPs