SNVPhyl Versions

This describes the different release versions of SNVPhyl.

Version 1.0

Released on May 25, 2016.

Install

• Docker - apetkau/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 - apetkau/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 - apetkau/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