Chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons.

References:

• Pérez-Wohlfeil, E., Diaz-del-Pino, S. & Trelles, O. Ultra-fast genome comparison for large-scale genomic experiments. Scientific reports 9, no. 1 (2019): 1-10.

• Chromeister Main Site

• Module Name: chromeister (see the modules page for more information)
• Multithreaded
• Environment variables set
  • CHROMEISTER_HOME
  • SCRIPTS adds scripts from /usr/local/apps/chromeister/1.5.a/scripts to path

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
[user@cn4274 ~]$ module load chromeister
[+] Loading chromeister  1.5.a  on cn4274
[+] Loading singularity  3.10.5  on cn4274
[+] Loading gcc  11.3.0  ...
[+] Loading HDF5  1.12.2
[+] Loading netcdf  4.9.0
[-] Unloading gcc  11.3.0  ...
[+] Loading gcc  11.3.0  ...
[+] Loading openmpi/4.1.3/gcc-11.3.0  ...
[+] Loading pandoc  2.18  on cn4274
[+] Loading pcre2  10.40
[+] Loading R 4.3.0

Execute Chromeister binary

#copy over test-data
[user@cn4274 ~]$ cp -a /usr/local/apps/chromeister/test-data .
[user@cn4274 ~]$ cd test-data
#run chromeister with inputs
[user@cn4274 test-data]$ CHROMEISTER -query mycoplasma-232.fasta \
-db mycoplasma-232.fasta \
-out mycoplasma-232-7422.mat \
-dimension 500 && Rscript ${SCRIPTS}/compute_score.R mycoplasma-232-7422.mat 500
[INFO] Generating a 500x500 matrix
[INFO] Loading database
99%...[INFO] Database loaded and of length 892758.
[INFO] Ratios: Q [1.785516e+03] D [1.785516e+03]. Lenghts: Q [892758] D [892758]
[INFO] Pixel size: Q [5.600622e-04] D [5.600622e-04].
[INFO] Computing absolute hit numbers.
99%...Scanning hits table.
99%...
[INFO] Query length 892758.
[INFO] Writing matrix.
[INFO] Found 25819 unique hits for z = 4.
0

Annotate an SV:

[user@cn4338] cp -a /usr/local/apps/duphold/0.2.3/test_data .
[user@cn4338 test_data]$ duphold \
 --threads 4 \
 --vcf sparse_in.vcf \
 --bam sparse.cram \
 --fasta sparse.fa \
 --output output.bcf 
#To view output, load samtools and view with bcftools
[user@cn4338 test_data] module load samtools
[user@cn4338 test_data] bcftools view test-out.bcf
##fileformat=VCFv4.2
...
##bcftools_viewVersion=1.4-19-g1802ff3+htslib-1.4-29-g42bfe70
##bcftools_viewCommand=view CHM1_CHM13/full.37d5.vcf.gz; Date=Mon Sep 24 13:48:04 2018
...
##bcftools_viewVersion=1.17+htslib-1.17
##bcftools_viewCommand=view test-out.bcf; Date=Thu May 25 12:49:34 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  Eluc-CR2.F
NW_017858824.1  135118  72454   N       DEL   5875.46 .       SVTYPE=DEL;END=135332;CIPOS=0,0;CIEND=0,0;CIPOS95=0,0;CIEND95=0,0;GCF=0.306977  GT:DP:DHFC:DHFFC:DHBFC:DHSP     0/1:200:1.91667:0.597403:1.76923:0