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ampril-genomes

scripts for the project of seven thaliana genomes assembly

ampril-gi

The scripts used in the project "The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana"

apricot_layer_mutations

chromodo

Toolbox for genome assemblies and chromosomes

drlink

Detecting recombination breakpoints using Linked read sequencing

findgse

findGSE is a tool for estimating size of (heterozygous diploid or homozygous) genomes by fitting k-mer frequencies iteratively with a skew normal distribution model.

fixchr

gametebinning

gametebinning_prac

Here are the codes for a practice of gamete binning with simulated data

gametebinning_tetraploid

This is used to achieve haplotype-resolved assembly of tetraploid genomes using gamete sequencings

genomevar

Identification of genomic differences from whole-genome alignments

hexaploid_ma_lines

scripts pertaining to analysis of the hexaploid mutation accumulation lines

msyd

plotsr

Tool to plot synteny and structural rearrangements between genomes

rtiger

scripts_supporting_kiefer_willing_et_al_2019

Scripts_supporting_Kiefer_Willing_et_al_2019

shoremap_v3.x

snrna_eqtl_mapping

Pipeline for processing 10X snRNAseq data to map eQTLs in recombinant gametes

syri

Synteny and Rearrangement Identifier

toolbox