Tool to quickly make a minimalistic 600x600 pixels heatmap image of read length (log-transformed) and read accuracy.
| Gap-compressed percent identity | Phred-scale accuracy | Comparison of two runs |
|---|---|---|
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Download the appropriate binary from the releases.
Usage: kyber [OPTIONS] <INPUT>
Arguments:
<INPUT> cram or bam file, or use `-` to read from stdin
Options:
-t, --threads <THREADS> Number of parallel decompression threads to use [default: 4]
-o, --output <OUTPUT> Output file name [default: accuracy_heatmap.png]
-c, --color <COLOR> Color used for heatmap [default: green] [possible values: red, green, blue, purple, yellow]
-b, --background <BACKGROUND> Color used for background [default: black] [possible values: black, white]
-p, --phred Plot accuracy in phred scale
--normalize Normalize the counts in each bin with a log2
-h, --help Print help
-V, --version Print version
Both the x and y axis are fixed, allowing for comparison across datasets. The current settings should work for most (long-read) datasets, let me know if you disagree. The x-axis has log transformed read lengths, with a maximum length of 1M. The y-axis has the gap-compressed reference identity, ranging from 70% to 100%. When using Phred-scaled accuracy scores, the y-axis ranges from Q0 to Q40.
A 150 gigabase BAM file (from ONT PromethION) is processed in 11 minutes using 4 decompression threads (the default). If your input dataset is very large, you may want to consider to downsample it with samtools view -h and pipe that to kyber, e.g. samtools view -h -s 0.05 alignment.cram | kyber -
If you use this tool, please consider citing our publication.