Name: Xu Cai
Type: User
Company: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science
Bio: I am a postdoctoral researcher at the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, focusing on genomic analysis of Brassica.
Location: 12 Zhongguancun Nandajie, Haidian, Beijing 100081, China
Xu Cai's Projects
Scripts used for Brassica rapa gene model prediction
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
CNV calling method based on assembly and read depth of NGS data
conserved non-coding sequence
DensityMap is perl tool for the visualization of features density along chromosomes
它是一个工作流。可快速构建指定架构/平台的docker镜像
Extensive de-novo TE Annotator
Compare different genome alignment tools using a wide range of genomes with different complexities.
GSAlign: an ultra-fast sequence alignment algorithm for intra-species genome comparison
Identification of transposable element insertion polymorphisms (TIPs) based on a pan-genome and large-scale resequencing data
Python utility libraries on genome assembly, annotation and comparative genomics
Micro-syntenic plot of two and more genomic segments
An automated misjoins correction pipeline (named MisjoinDetect) based on Hi-C data
my perl scripts
Phylogenetic Analysis of Long Terminal Repeat Retrotransposons
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
RelocaTE2
The code used in the manuscript titled "Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants".
Toolkit for processing sequences in FASTA/Q formats
Synteny and Rearrangement Identifier
《蓝眼云盘》(Eyeblue Cloud Disk)
Algorithm to detect germline and de novo transposon insertions