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cafe5

Version 5 of the CAFE phylogenetics software

cdna_cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

chloroplast-genome-assembly

A pipeline for assemble chroloplast genome using short/long reads

deepconsensus

DeepConsensus uses gap-aware sequence transformers to correct errors in Pacific Biosciences (PacBio) Circular Consensus Sequencing (CCS) data.

dnngp

DNNGP: Deep neural network for genomic prediction

easy_marker

edta

Extensive de-novo TE Annotator

estimate_genome_size.pl

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

genelift

Gene model transfer from closely related reference genomes using cDNA alignments

huasmalltools

Some bioinformic domestic scripts.

kat

The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.

ldblockshow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

ldhat

Estimate recombination rates from population genetic data

mapviewer

Integration and visualization of genetic maps

merqury

k-mer based assembly evaluation

my-script

myscripts

nlr-parser

Annotation Pipeline for NLR genes

phasebook

Haplotype aware de novo assembly of diploid genome from long reads

pigbs_pipeline

Parent-independent genotyping of diploid potato

popcnv

pseudogenepipeline

public

pyrho

Fast inference of fine-scale recombination rates based on fused-LASSO

quartet

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

rumex_genome

Scripts for publication with the Rumex genome paper

sexphase

slc_id_scripts

smartie-sv

calling SVs from Blasr contig level alignments

snap

Gene prediction software