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mrvollger/StainedGlass

Make colorful identity heatmaps of genomic sequence

Overview​

Topics:

Latest release: v0.6, last update: 2025-01-23

Linting: passed

Formatting: passed

Configuration​

Configuration options​

Below are the options that can be changed in config.yaml.

A sample/prefix identifier to append to your result files

sample: test

Path to a fasta file to deploy the workflow on

fasta: .test/small.fasta

Size of the window in which to breakup the input fasta before all by all alignment.

window: 5000

Setting for the minimap2 -f parameter. A smaller number will increase sensitivity at the cost of runtime. See the minimap2 man page for more details.

mm_f: 10000

The number of alignment jobs to distribute the workflow across. Does not change final output.

nbatch: 1

The number of alignment threads per job.

alnthreads: 4

Path for a temp dir to be used by pipeline.

tempdir: temp

Configuration options for high-res dot plots (cooler_density)​

This defines the smallest bin size (highest resolution) used in the cooler file.

cooler_window: 100

Since window defines the read length, it should be made to be smaller than cooler_window. I like to use window: 32 and cooler_window: 100.

This is the maximum number of alignments to output for each read. From the bwa help page: Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written.

num_dups: 100