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3.6.20231115
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@erinyoung erinyoung released this 17 Nov 18:35
· 286 commits to main since this release
v3.6.20231115
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Learn about vigilant mode.

Notable changes:

  • updated blast to 2.14.1
  • updated quast to 5.2.0
  • added a heatcluster process that takes the SNP matrix from SNP dists and visualizes it

heatcluster

  • added a phytreeviz process that takes the newick file from iqtree2 and visualizes it

tree

  • added a process to better evaluate the core genome

An example file:

sample,total,core,soft,shell,cloud,per_core,per_soft,per_shell,per_clouc,length,num_ambiguous,per_ambiguous
GCF_000834105.1_ASM83410v1_genomic,776.0,284.0,0.0,309.0,183.0,0.36597938144329895,0.0,0.39819587628865977,0.23582474226804123,275096.0,2750.0,0.00999651030912845
GCF_000972335.1_ASM97233v1_genomic,892.0,284.0,0.0,350.0,258.0,0.3183856502242152,0.0,0.3923766816143498,0.289237668161435,275096.0,6260.0,0.022755692558234217
GCF_000788095.1_ASM78809v1_genomic,3892.0,284.0,0.0,3431.0,177.0,0.07297019527235354,0.0,0.881551901336074,0.045477903391572455,275096.0,4121.0,0.014980225085061215
SRR14436834,3965.0,284.0,0.0,3512.0,169.0,0.07162673392181589,0.0,0.885750315258512,0.04262295081967213,275096.0,5720.0,0.020792741442987175
GCF_900475405.1_44087_C01_genomic,3987.0,284.0,0.0,3567.0,136.0,0.07123150238274392,0.0,0.8946576373212942,0.03411086029596187,275096.0,3272.0,0.011894029720533923
GCF_000758465.1_ASM75846v1_genomic,4017.0,284.0,0.0,3368.0,365.0,0.07069952701020663,0.0,0.838436644261887,0.0908638287279064,275096.0,3497.0,0.012711926018553523
GCF_000978875.1_ASM97887v1_genomic,4189.0,284.0,0.0,3620.0,285.0,0.06779661016949153,0.0,0.8641680592026737,0.0680353306278348,275096.0,5192.0,0.018873411463634512
GCF_000742995.1_ASM74299v1_genomic,4551.0,284.0,0.0,3722.0,545.0,0.06240386728191606,0.0,0.8178422324763788,0.11975390024170512,275096.0,3023.0,0.010988891150725565
  • removed the heatcluster python script since heatcluster has a standalone github repo
  • !!! CHANGED THE NAME OF A PARAMETER : params.roary_min_genes is now params.min_core_genes !!!
    • this suggests that there will be changes coming to the phylogenetic analysis subworkflow

Non-notable changes:

  • add myco_flag for Mycobacterium (am still in the processing of testing modules)
  • added drprg, mykrobe, and mashtree processes that aren't connected to anything
Assets 2
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