Command Line tools

The following tools use BAM files as input. These BAM files could can from any single-cell genomics protocol, as long as they have a tag that specifies the cell barcodes.

• scFilterBarcodes

• scFilterStats

• scCountReads

• scBulkCoverage

• scJSD

The following tools use the AnnData output produced within the sincei analysis workflow, with file extension .h5ad.

• scCountQC

• scCombineCounts

• scClusterCells

The table below summarizes input and output of each tool:

tool	type	input files	main output file(s)	application
scFilterBarcodes	preprocessing	BAM/SAM files	text file with filtered cell barcodes	Identify and filter cell barcodes (for droplet-based single-cell seq)
scFilterStats	QC	BAM/SAM files	text file with QC per cell	Produce per-cell statistics after filtering reads by user-defined criteria.
scCountReads	preprocessing	BAM/SAM files	h5ad object with cellxregion counts	Counts reads for each barcode on genomic bins or user-defined features.
scCountQC	QC	h5ad object	QC metrics / filtered h5ad file	Perform quality control and filter the output of scCountReads.
scCombineCounts	preprocessing	h5ad objects	merged h5ad object	Concatenate/merge the counts from different samples/batches or modalities
scClusterCells	analysis	h5ad object	.tsv file with clusters, png with UMAP	Perform dimensionality reduction and clustering on the output of scCountReads.
scBulkCoverage	analysis	tsv file + BAM file	bigwig files	Get pseudo-bulk coverage per group using a user-supplied cell->group mapping (output of scClusterCells).