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3d-dna

3D de novo assembly (3D DNA) pipeline

astral

Accurate Species TRee ALgorithm

cebai

centromics

Centromics: visualing centromeres with multiple omics data

circlator

A tool to circularize genome assemblies

degeneracy

Get 0-fold and 4-fold degeneracy sites

evolution_example

Example for evlutionary analyses with Orthology Index

fbpolisher

polishing noisy genome assembly with short reads of high-quality

kmc

Fast and frugal disk based k-mer counter

matplotlib

matplotlib: plotting with Python

mgra

microbephylogenomics

A pipeline to construct phylogenomic tree for microbial genomes

minimap2

A fast pairwise aligner for genomic and spliced nucleotide sequences

mysql2sqlite

Converts MySQL dump to SQLite3 compatible dump

nextpolish

Fast and accurately polish the genome generated by noisy long reads.

oak

ogap

OGAP: Organelle Genome Annotation Pipeline

orthoindex

Robust identification of orthologous synteny with the Orthology Index

phytop

Visualing species tree from ASTRAL with gene tree discordance

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

repcluster

Clustering repeat sequences with kmer-based distance

runcmdsmp

Run system commands parallelly

scripts

smartdenovo

Ultra-fast de novo assembler using long noisy reads

subgenome_phasing_example

An Example of Subgenome Phasing for Complex Allopolyploidy

subphaser

Phase, partition and visualize subgenomes of a neoallopolyploid or hybrid based on the subgenome-specific repetitive kmers.

syri

Synteny and Rearrangement Identifier

tesorter

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

unanimity

Consensus library and applications

unicycler

hybrid assembly pipeline for bacterial genomes