Software

Our code is developed under vollgerlab and fiberseq on GitHub.

Tools

fibertools-rs

Rust★ 64

CLI and library for processing Fiber-seq data.

GitHub Docs Paper

rustybam

Rust★ 101

A bioinformatics toolkit in Rust for processing alignments.

GitHub Docs Paper

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FIRE

Python★ 29

Snakemake workflow for calling Fiber-seq Inferred Regulatory Elements (FIREs) on single molecules.

GitHub Docs Paper

Visualization

StainedGlass

HTML★ 128

Interactive visualization of tandem repeat structures with identity heatmaps.

GitHub Docs Paper

SafFire

JavaScript★ 31

Interactive tool for visualizing alignments between genomes.

GitHub Docs Paper

NucFreq

Python★ 38

Visualize collapses in de novo assemblies.

GitHub Docs Paper

Workflows

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Rhodonite

Perl★ 4

A modular workflow for sequence masking and annotation.

GitHub Docs

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hap-windows

Python★ 2

Extract haplotype-specific sequences centered on BED intervals from phased VCFs.

GitHub

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k-mer-variant-phasing

Python★ 10

K-mer based variant phasing.

GitHub

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asm-to-reference-alignment

R★ 7

Assembly-to-reference alignment pipeline.

GitHub

fastCN-smk

Python★ 4

Snakemake workflow for fastCN copy number estimation.

GitHub

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asm-smk

Python★ 2

Assembly Snakemake workflow.

GitHub

Tutorials

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SmkTemplate

Python★ 43

A template for publication quality Snakemake workflows.

GitHub Docs

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