Phylogenetic orthology inference for comparative genomics

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Inferring CNV from Single-Cell RNA-Seq

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data

Copy number variant detection from targeted DNA sequencing

Mapping out the coarse-grained connectivity structures of complex manifolds.

Official code repository for GATK versions 4 and up

A toolkit for prokaryotic comparative genomics

AnnData interoperability in R

a python extension of CNVnator -- a tool for CNV analysis from depth-of-coverage by mapped reads

ASCAT R package

Structural variation caller using third generation sequencing

scripts for the integrating ATAC-seq, RNA-seq and CHi-C paper

Pod5: a high performance file format for nanopore reads.

Oxford Nanopore's Basecaller

Interfaces for HDF5-based Single Cell File Formats

Master the command line, in one page

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

Bayesian Evolutionary Analysis Sampling Trees

An analysis pipeline for long-reads from both PacBio and Oxford Nanopore Technologies (ONT), written in Nextflow.

PhyML -- Phylogenetic estimation using (Maximum) Likelihood

SRA Tools

A tool for somatic structural variant calling using long reads

Sequence correction provided by ONT Research

SingleCell Nanopore sequencing data analysis

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions