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jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

ka_ks_pipe

kineticstools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

kinfin

Taxon-aware analysis of clustered protein sequences

lantern

蓝灯(Lantern)破解

mcmctree

Bayesian estimation of species divergence times

meteore

Automatic DNA methylation detection from nanopore tools and their consensus model

mummer

Mummer alignment tool

netomics

Multi-omics multi-layered network integration and interpretation

netomics-case-studies

oak

ogap

OGAP: Organelle Genome Annotation Pipeline

orthoindex

Robust identification of orthologous synteny with the Orthology Index

paraat

pbsv

pbsv - PacBio structural variant (SV) calling and analysis tools

pipeline-nanopore-ref-isoforms

Pipeline for annotating genomes using long read transcriptomics data with stringtie and other tools

plantpseudo

population_genomics_scripts

Scripts used for population genomics projects

rad_tools

A collection of usefull tools for RAD or GBS data analysis

rna-seq-analysis

RNAseq analysis notes from Ming Tang

samplot

Plot structural variant signals from many BAMs and CRAMs

scorpios

SCORPiOs is a synteny-guided gene tree correction pipeline for clades that have undergone a whole-genome duplication event.

scripts_for_gb

The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".

smartie-sv

calling SVs from Blasr contig level alignments

sniffles

Structural variation caller using third generation sequencing

subphaser

Phase and visualize subgenomes of an allopolyploid or hybrid based on the repetitive kmers.

svmu

A program to call variants from genome alignment

syri

te_discovery

A comprehensive annotation of transposable elements in potato genome

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.