SNVPhyl Versions
This describes the different release versions of SNVPhyl.
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