From: hadge: a comprehensive pipeline for donor deconvolution in single-cell studies
Demuxafy | cellHashR | HTOreader | hadge | |
---|---|---|---|---|
Framework | Singularity | R | R | Nextflow |
Available genotype-based methods | 5 | - | Souporcell | 5 |
Available hashing-based methods | - | 7 | HTOreader | 7 |
Doublet detection methods | 7 | - | - | 1 |
Concatenating | - | - | -(*) | + |
Parallelized | - | - | - | + |
Pre-processing tools | Samtools (*) | ProcessCountMatrix, PlotNormalizationQC | HTOClassification | Samtools |
Variant calling tools | Freebayes(*), cellSNP-lite (*) | (not relevant for hashing-based) | (not relevant for hashing-based) | Freebayes, cellSNP-lite |
Associating clusters and donors | Only through reference SNP genotypes | (not relevant for hashing-based) | From hashtags to donors based on confusion matrix | From hashtags to donors based on matching Phi score |
Combining results | + | + | - | + |
scverse compatibility | - | - | - | + |