Tools

fibertools

The toolkit for processing Fiber-seq data. fibertools

Segmental Duplication Assembler (SDA) is for identifying and resolving collapsed SDs.
SDA

A toolkit for processing alignments. Works well with SafFire.
Rustybam

A modular workflow for sequence masking and annotation.
Rhodonite

Identity heatmaps from alignments.
StainedGlass

SafFire is a tool for visualizing alignments between genomes. It serves as a interactive replacement for miropeats.
SafFire

Visualize collapses in de novo assemblies.
NucFreq

For visualizing de novo assemblies against a karyotype of the human reference.
Ideogram

A template for for publication quality snakemake workflows (slides). SmkTemplate