piranha v1.0.6

• Plate vizualization showing positives along the plate. #103
• Ability to map barcodes vertically or horizontally along the plate with the --orientation flag, or can read from the barcodes.csv. #103
• introducing medaka_haploid_variant pipeline for variant calling and stitching together with medaka stitch. #62
• variation plot now only shows high quality base variants (>13) and code for parsing from the bam file from @Desperate-Dan #96
• cooccurrance analysis now also parsed from bam, so no need for construction of pseudoalignment (also only uses high quality bases for cooccurrance analysis now too) #107
• new cooccurrance plot, as heatmap rather than barplot #97
• read trimming for primer removal #101

piranha v1.0.5

• Fasta links fixed (Issue #91)
• Additional downloadable wide format report (Issue #92)
• Flag for stool or env samples, only flag table about NonPolioEV if env sample (Issue #85 #83 )
• No temp and wpv3 descriptions in read me (#84 #85), actually a lot of extra info in the readme now (#80)
• #21 snipit plots will now display indels too
• #34 ref in database will display in wide format report
• Raw fastq sequences now in published dir (#63)
• Classification and pcent match stats in wide csv too (#93)
• piranha available on bioconda thanks to @rpetit3 under piranha-polio. Installation should work with:

mamba install -c bioconda piranha-polio

piranha v1.0.4

Added qc requested into report and embeded fasta sequences

piranha v1.0.3

Fix for issue flagged in #66.

piranha version 1.0

Initial release of piranha repository, with VP1 protocol enabled and report generation.