SmartSeq2SingleSample_v5.1.21

5.1.21

2024-09-11 (Date of Last Commit)

• Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the SmartSeq2SingleSample pipeline

SlideSeq_v3.4.2

3.4.2

2024-09-24 (Date of Last Commit)

• Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; this does not impact the slideseq workflow

PairedTag_v1.7.0

1.7.0

2024-09-24 (Date of Last Commit)

• Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
• Updated gene_names in the final h5ad to be unique

Optimus_v7.7.0

7.7.0

2024-09-24 (Date of Last Commit)

• Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
• Updated gene_names in the final h5ad to be unique

Multiome_v5.7.0

5.7.0

2024-09-24 (Date of Last Commit)

• Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; percent doublets are now available as a library-level metric and individual doublet scores for cell barcodes are in the h5ad
• Updated gene_names in the final h5ad to be unique

MultiSampleSmartSeq2_v2.2.22

2.2.22

2024-09-11 (Date of Last Commit)

• Updated warp-tools docker which added create_h5ad_snss2.py to the docker image. This change does not affect the MultiSmartSeq2 pipeline

MultiSampleSmartSeq2SingleNucleus_v2.0.1

2.0.1

2024-09-24 (Date of Last Commit)

• Added a python implementation of DoubletFinder to calculate doublet scores in gene expression data; this does not affect the snSS2 workflow

JointGenotyping_v1.7.1

1.7.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling
• If target interval list is provided for filtering, the documentation in the header will be clearer
• If VETS is enabled, the SCORE annotation will be added to all output variants (even hard filtered sites)

JointGenotypingByChromosomePartTwo_v1.5.1

1.5.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling; this has no effect on this pipeline

JointGenotypingByChromosomePartOne_v1.5.1

1.5.1

2024-09-10 (Date of Last Commit)

• Update to BGE filtering options in JointCalling; this has no effect on this pipeline