Commands:

add_uid

Adds UID:[samplebc cellbc umi] to readname for...

bamtag

Convert a BAM/SAM with fastqtransformed read names to...

cb_filter

Filters reads with non-matching barcodes Expects...

cb_histogram

Counts the number of reads for each cellular barcode...

demultiplex_cells

Demultiplex a fastqtransformed FASTQ file into a...

demultiplex_samples

Demultiplex a fastqtransformed FASTQ file into a...

fastqtransform

Transform input reads to the tagcounts compatible...

fasttagcount

Count up evidence for tagged molecules, this...

kallisto

Convert fastqtransformed file to output format...

mb_filter

Filters umis with non-ACGT bases Expects formatted...

sb_filter

Filters reads with non-matching sample barcodes...

sparse

Convert a CSV file to a sparse matrix with rows and...

subset_bamfile

Subset a SAM/BAM file, keeping only alignments from...

tagcount

Count up evidence for tagged molecules

umi_histogram

Counts the number of reads for each UMI Expects...

version