Releases: dmnfarrell/snipgenie
Releases · dmnfarrell/snipgenie
v0.7.0
- changed calling step to now run mpileup and call separately. now merge called vcfs at end, allows re-running pipeline much easier
- 16S species check plugin
- added calling_method option to allow use of old calling method
- changed proximity filter to number, now default unless value is 0
- check for duplicates tool allows dups to be marked
- move fastq file option
- snp tables should now display better with vertical column header
- removed rtd docs - moved to wiki
v0.6.1
Last release using old mpileup/calling method.
- fixes to RD plugin
- fixes to contam plugin
- added assembly plugin
- quality check in gui
v0.6.0
- fix to pair order in sample names when pivoted
- fix to keeping unmapped reads when not needed
- check samples match a previous raw.bcf file when running
- plugin system for gui
- gui - contam plugin added
- gui - testing plugin
- added manifest file option to cmd line
- removed get samples from bams during workflow, redundant
v0.5.0
- changed sample table format to single rows per sample
- fixes to RD analysis
- added minimap2 aligner for ont reads
- added platform keyword if using ont
- settings in gui saved
- mask in preset for gui
- redirect stdout to log in gui
- fixed spotyping
v0.4.0
- changes to output files, snps and indels now output
- snps file made after filtering of calls
- make tree with snp branch lengths
- can save unmapped reads
- some gui fixes
v0.3.0
- can mask sites with bed file
- fix to use only core snps
- can remove uninformative sites from core
- can create qc report from cmd line
- more preset preset genomes
- can select species at command line
- added subread aligner
- map view for gui
- gui tree viewer
- spoligotyping tool to gui
- find heterozygous sites
- plot snp matrix
- changed name to snipgenie
v0.2.0
- improved vcf to fasta sites method
- renamed to snpgenie
- use genbank as annotation file
- added proximity filter
- GUI works for any ref genome
- text bam alignment viewer
- add folders in gui
- clean up files option
- fastq qualities report
v0.1.0
- first version
- CLI workflow works for general microbial genomes
- GUI works for mbovis so far
- functions working so far: trimming, alignment, variant calling, snp matrix, tree building