SNVPhyl Versions

This describes the different release versions of SNVPhyl.

Version 1.1.0

Released on June 6, 2019.

Install

• Docker - phacnml/snvphyl-galaxy-1.1.0
• Galaxy Tools - suite_snvphyl_1_1_0
• Galaxy Workflows
  • Paired-end: SNVPhyl Paired-End 1.1.0 and SNVPhyl Paired-End 1.1.0 (invalid-positions)
  • Single-end: SNVPhyl Single-End 1.1.0 and SNVPhyl Single-End 1.1.0 (invalid-positions)
• Git - https://github.com/phac-nml/snvphyl-galaxy/tree/1.1.0

Changelog

• Convert all SNVPhyl wrappers from tool shed package to bioconda (v1.8.2)
• Removed following unused/deprecated wrappers & capsules
  • Wombac
  • Seqtk NML
  • package_perl_5_18_iuc
  • package_msa_datatypes_iuc
  • package_mummer_3_23
  • bcf_bgzip
• Removed following wrappers that are now available on main public tool shed
  • smalt
  • freebayes
  • bcftools mpileup
  • phyml
  • bcftools view
  • bcftools call
• Enable CI testing with Travis

Version 1.0.1

Released on January 23, 2017.

Install

• Docker - phacnml/snvphyl-galaxy-1.0.1
• Virtual Machine - snvphyl-galaxy-1.0.1.zip
• Galaxy Tools - suite_snvphyl_1_0_1
• Galaxy Workflows
  • Paired-end: SNVPhyl Paired-End 1.0.1 and SNVPhyl Paired-End 1.0.1 (invalid-positions)
  • Single-end: SNVPhyl Single-End 1.0.1 and SNVPhyl Single-End 1.0.1 (invalid-positions)
• Git - https://github.com/phac-nml/snvphyl-galaxy/tree/1.0.1

Changelog

• Re-named parameter alternative-allele-ratio to snv-abundance-ratio.
• Added tool positions2snv_alignment to Galaxy to generate an alignment of only variant-containing positions.
• Added tool positions2snv_invariant_alignment to Galaxy to generate an alignment of all (variant or non-variant) positions.
• Updated density window size parameter to a default value of 500.
• Updated download location of dependency package_zlib_1_2_8.
• Formatting/text changes to some Galaxy tools.

Version 1.0

Released on May 25, 2016.

Install

• Docker - phacnml/snvphyl-galaxy-1.0
• Virtual Machine - snvphyl-galaxy-1.0.zip
• Galaxy Tools - suite_snvphyl_1_0_0
• Galaxy Workflows
  • Paired-end: SNVPhyl Paired-End 1.0 and SNVPhyl Paired-End 1.0 (invalid-positions)
  • Single-end: SNVPhyl Single-End 1.0 and SNVPhyl Single-End 1.0 (invalid-positions)
• Git - https://github.com/phac-nml/snvphyl-galaxy/tree/v1.0

Changelog

• Additions
  • Added ability to remove high-density SNV regions by adjusting a window size and threshold of SNVs.
  • Added additional information to the vcf2core.tsv output file.
  • Added workflows for single-end sequence read data.
  • Re-named many internal scripts to use terminology of SNV alignment instead of pseudoalignment.
• Fixes
  • Fixed output of filterStats.txt to include invalid positions.
  • Additional checks to verify depth of coverage for invariant sites.
  • Fixed behaviour of of tools like bcftools to enable re-scheduling within a cluster when run through Galaxy by ignoring existing output file.
  • Fixed up issues with incorrect/missing dependencies among tools in Galaxy.

Version 0.3

Released on November 13, 2015.

Install

• Docker - phacnml/snvphyl-galaxy-0.3
• Virtual Machine - snvphyl-galaxy-0.3.zip
• Galaxy Tools - suite_snvphyl_0_3_0
• Galaxy Workflow - SNVPhyl Paired-End 0.3 and SNVPhyl Paired-End 0.3 (invalid-positions)
• Git - https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy/tree/v0.3

Changelog

• Updated git URLs to reference new gitlab https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy.
• Updated FreeBayes to refer to latest version in Galaxy freebayes_0_9_20_b040236
• Updated samtools sort to use multiple threads.
• Made Do not perform INDEL calling the default for SAMtools mpileup.

Version 0.2-beta-1

Released on September 21, 2015.

Install

• Docker - phacnml/snvphyl-galaxy-0.2-beta-1
• Virtual Machine - snvphyl-galaxy-0.2-beta-1.zip
• Galaxy Tools - suite_snvphyl_0_2_0
• Galaxy Workflow - SNVPhyl Paired-End 0.2 and SNVPhyl Paired-End 0.2 (invalid-positions)
• Git - https://irida.corefacility.ca/analysis-pipelines/snvphyl-galaxy/tree/v0.2-beta-1

Changelog

• Initial release of SNVPhyl run through Galaxy
• Includes Docker and Virtual Machine images
• Mapping/variant calling, variant merging, constructing phylogeny
• Quality checking tools for coverage, % of core used, and variants filtered