biosiftr - v1.2.1

What's Changed

• Updating master branch by @Ales-ibt in https://github.com/EBI-Metagenomics/biosiftr/pull/13
• Debug/dram html by @Ales-ibt in https://github.com/EBI-Metagenomics/biosiftr/pull/18
• Pipeline nf-test by @Ales-ibt in https://github.com/EBI-Metagenomics/biosiftr/pull/19
• Adjust the download references to work with S3 storage by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/20
• Bugfix/correct master dev discrepancies by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/22
• Prep for new minor release by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/21
• Bugfix/correct master dev discrepancies by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/23
• I've changed how the DRAM db is used in distill by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/24
• Fix some versions naming issues and removed redudant cat on awk command by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/25
• Update master - preparing for a new release by @mberacochea in https://github.com/EBI-Metagenomics/biosiftr/pull/26

Full Changelog: https://github.com/EBI-Metagenomics/biosiftr/compare/v1.2.0...v1.2.1

- Python
Published by mberacochea 12 months ago

biosiftr - BioSIFTR v1.2.0

The name of the pipeline has changed from Shallowmapping to BioSIFTR

• The optimisation of bwa-mem2 is dynamic #12
• The generation of DRAM visuals is optional #11
• A subworkfow was added to download the databases #8 and #9
• This version can be run with the following biomes available in MGnify Genomes catalogues: chicken-gut v1.0.1 cow-rumen v1.0.1 human-gut v2.0.2 human-oral v1.0.1 human-vaginal v1.0 honeybee-gut v1.0.1 marine v2.0 mouse-gut v1.0 non-model-fish-gut v2.0 pig-gut v1.0 sheep-rumen v1.0 zebrafish-fecal v1.0

- Python
Published by Ales-ibt about 1 year ago

biosiftr - Version v1.1.0

What's Changed

• Fix linting problems. by @mberacochea in https://github.com/EBI-Metagenomics/shallowmapping/pull/2
• Dram fixes by @Ales-ibt in https://github.com/EBI-Metagenomics/shallowmapping/pull/3
• PR to update optimised params and remove bams after bwamem alignment by @Ales-ibt in https://github.com/EBI-Metagenomics/shallowmapping/pull/4
• Fix a string comparison that was causing the pipeline to crash. by @mberacochea in https://github.com/EBI-Metagenomics/shallowmapping/pull/5

Added support for the human-gut-v2-0-2 biome.

Full Changelog: https://github.com/EBI-Metagenomics/shallowmapping/compare/v1.0.0...v1.1.0

- Python
Published by mberacochea almost 2 years ago

biosiftr - Shallow-mapping pipeline v1.0.0

This release of the pipeline can be run with the following biomes: - chicken-gut-v1-0-1 - mouse-gut-v1-0 - human-gut-v2-0-2

Other biomes can be supported under request by raising an issue in this repo.

Sourmash is the default tool to generate taxonomic profiles. Optionally, bwamem2 can be used as well. Pangenome function tables are used by default to generate functional profiles. Core functions can be used as well.

Databases are downloaded using the bash script provided. MGnify hosts all DBs needed, so the user doesn't need to generate them from scratch.

- Python
Published by Ales-ibt over 2 years ago