sc_seqLogo.py¶

Generate a DNA sequence logo from FASTA or FASTQ format files. Useful for visualizing nucleotide composition of sample barcodes, cell barcodes, and molecular barcodes (UMIs).

Usage¶

sc_seqLogo.py -i barcodes.fq -o output_prefix

Options¶

Option	Description	Default
`-i`, `--infile`	Input file in FASTQ, FASTA, or plain sequence format (plain text or gzip/bzip2 compressed)	Required
`-o`, `--outfile`	Prefix of output files	Required
`--iformat`	Input format: `fq` or `fa`	fq
`--oformat`	Output format: `pdf`, `png`, or `svg`	pdf
`-n`, `--nseq-limit`	Maximum number of sequences to process	All
`--font-name`	Logo font: `sans`, `serif`, `mono`, etc.	sans
`--stack-order`	Stacking order: `big_on_top`, `small_on_top`, `fixed`	big_on_top
`--flip-below`	Flip characters below X-axis upside down	Off
`--shade-below`	Shading amount for below-axis characters (0.0–1.0)	0.0
`--fade-below`	Fading amount for below-axis characters (0.0–1.0)	0.0
`--excludeN`	Exclude sequences containing N	Off
`--highlight-start`	Start position for highlighted region	None
`--highlight-end`	End position for highlighted region	None
`--verbose`	Print detailed debugging information	Off

Output¶

Sequence logo file in the specified format.