Kmeres v1.0

Kmeres - Identification of Centromeres and Telomeres using Kmer Profiles

Download and Compile:

$ git clone  https://github.com/wtsi-hpag/Kmeres.git 
$ cd Kmeres 
$ make

Run the pipelines

Run kmeres:

       $ /nfs/users/nfs_z/zn1/src/kmeres/kmeres hash -kmer 31 -sample Human CHM13v2.fa meres.fa  > cover.out \
       
       Parameters:
         kmer:         Size of kmer word  [ default = 31 ]
         sample:       Sample name 
         CHM13v2.fa:   Input genome assembly file 
         meres.fa:     Output centromere sequence file 

Test dataset:

A test dataset on the T2T gemome assembly of Arabidopsis Thaliana has been put at

https://ftp.sanger.ac.uk/pub/users/zn1/assembly/Thaliana/

The detected centromeres are in meres.fa

egrep ">" meres.fa

Chr1_032540122_014841792_017131968_002290176 Chr2_022217084_003826368_006048000_002221632 Chr3_025743512_013595904_015736896_002140992 Chr4_021578073_004201344_006979392_002778048 Chr5_029480885_011829888_014220864_002390976

Chr1:
chromosome length 32540122
centromere starts from 14841792
centromere ends at 17131968
centromere length 2290176 \

The centromeres predected by Kmeres are very close to those detected by Chip-seq, see

Naish M. et al. 2021 "The genetic and epigenetic landscape of the Arabidopsis centromeres". Science. 2021;374:eabi7489. doi: 10.1126/science.abi7489.

The users may download the assembly and try it first with a local computer. Then conpare with the output files at the FTP site.

Please contact Zemin Ning ( zn1@sanger.ac.uk ) for any further information.