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annotation_pl

Scripts used for Brassica rapa gene model prediction

clustersploter

visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, directly modify almost all features in web browser by click the feature, fragments genome view

ctgref-cnv

CNV calling method based on assembly and read depth of NGS data

dcns

conserved non-coding sequence

densitymap

DensityMap is perl tool for the visualization of features density along chromosomes

dockertarbuilder

它是一个工作流。可快速构建指定架构/平台的docker镜像

edta

Extensive de-novo TE Annotator

genomealignment

Compare different genome alignment tools using a wide range of genomes with different complexities.

gsalign

GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison

itips

Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data

jcvi

Python utility libraries on genome assembly, annotation and comparative genomics

justorthologs

link_3d_dna_scfs_to_chromosomes

microsynplot

Micro-syntenic plot of two and more genomic segments

misjoindetect

An automated misjoins correction pipeline (named MisjoinDetect) based on Hi-C data

myperlscripts

my perl scripts

phyltr

Phylogenetic Analysis of Long Terminal Repeat Retrotransposons

poplddecay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

populus-genomic-consequences-of-hybridization

pseudogenepipeline

relocate2

RelocaTE2

scripts

scripts_for_gb

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

seqtk

Toolkit for processing sequences in FASTA/Q formats

split_genes

sv-cnv-studies

syri

Synteny and Rearrangement Identifier

tank

《蓝眼云盘》(Eyeblue Cloud Disk)

temp2

Algorithm to detect germline and de novo transposon insertions