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

lusSTR version 0.4

This release includes updates to lusSTR to accommodate the most recent changes to the STRait Razor config files updated in October 2020 (ForenSeqv1.25.config) and January 2021 (PowerSeqv2.1.config). The new config file resulted in changes to the PowerSeq coordinates for all but 2 of the STR loci (including autosomal, X- and Y-chromosome loci).

This version of lusSTR also no longer requires the inclusion of _STRaitRazor.txt in the name of individual STRait Razor output files.