xzhuo

transanno

accurate LiftOver tool for new genome assemblies

EDTA

Extensive de-novo TE Annotator

Severus

A tool for somatic structural variant calling using long reads

jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics

jstreeview

Interactive phylogenetic tree viewer/editor

MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

rust-bio

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

metheor

:comet: Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

fibertools-rs

Tools for fiberseq data written in rust.

awesome-markdown-editors

A collection of awesome markdown editors & (pre)viewers for Linux, Apple OS X, Microsoft Windows, the World Wide Web & more

ModDotPlot

JARVIS

JARVIS, a system to connect LLMs with ML community. Paper: https://arxiv.org/pdf/2303.17580.pdf

noodles

Bioinformatics I/O libraries in Rust

pb-CpG-tools

Collection of tools for the analysis of CpG data

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences

awesome-genome-visualization

A list of interesting genome browser or genome-browser-like implementations

comparative-selection-widget

Tree widget for selection of species for http://comparativegateway.wustl.edu

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

dorado

Oxford Nanopore's Basecaller

wgbs

snake file of wgbs pipeline

tldr

Identify and annotate TE-mediated insertions in long-read sequence data

methylartist

Tools for plotting methylation data in various ways

rustybam

bioinformatics toolkit in rust

ccsmeth

Detecting DNA methylation from PacBio CCS reads

vg

tools for working with genome variation graphs

odgi

Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs

wgbs

WGBS processing pipeline

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

pggb

the pangenome graph builder