BioNano-Irys-tools

tools to work with BioNano Irys optical maps (cmaps)

Bash (zsh) script to pick cmaps (by ID) from a multi-cmap file and invert (flip) selected. Then create a fused cmap from these (e.g. a chromosome). selected (incl flipped) cmaps are stored separately as well.

./cmap_pick_flip_merge.sh MAPIDs.lst GAPSIZE NEWID INCMAP.cmap OUTPREFIX  

Parameters are as follows.

MAPIDs.lst

• file containing list of cmap ID's to pick and/or flip (flip if negative) from a main optical.genome.assembly.cmap
• one entry per line, last line will not be used, thus leave as empty line
• eg fuse/orientate cmap-optical-contig 185+249+7+15+945 and turn around the contig 185,15 and 945

-185  
249  
7  
-15  
-945  

GAPSIZE

Gap to be used between two adjacent cmaps [bp] (i.e. number of Ns to fill with). E.g. for 50kb, use 50000

NEWID

ID [integer] for fused cmap (output), means cmap-ID within the cmap file. E.g. 1 (as in LG1 or chr1)

INCMAP.cmap

CMAP (v0.1) file containing multiple cmaps (optical_genome.cmap; input), ie the file from which the individuals cmaps are picked. E.g., Sinv_bigB.cmap.

If specific GAP-sizes for a specific location are needed, then add cmap entry to this cmap (with unique new ID) and adjust the MAPIDs.lst accordingly to incorporate a specific cmap-contig (which is empty=gap). Take into consideration that the general GAPSIZE is applied everywhere (also between contig and gap-contig), ie potentially adjust the size of the gap accordingly.

OUTPREFIX

Prefix used for output files. E.g. LG1

Example command

e.g. to contruct an optical chromosome 1 (LG1) from all optical contigs known to be on LG1 and in their respective order / orientation

files in folder

#ls -1  
cmap_pick_flip_merge.sh  
Sinv_bigB_all_unplaced_cmaps.lst  
Sinv_bigB.cmap  
Sinv_LG10.lst  
Sinv_LG11.lst  
Sinv_LG12.lst  
Sinv_LG13.lst  
Sinv_LG14.lst  
Sinv_LG15.lst  
Sinv_LG16.lst  
Sinv_LG1.lst  
Sinv_LG2.lst  
Sinv_LG3.lst  
Sinv_LG4.lst  
Sinv_LG5.lst  
Sinv_LG6.lst  
Sinv_LG7.lst  
Sinv_LG8.lst  
Sinv_LG9.lst  

command

i=1  
./cmap_pick_flip_merge.sh Sinv_LG$i.lst 50000 $i Sinv_bigB.cmap Sinv_bigB.$i  

output on screen

Output-Prefix: Sinv_bigB.1  
Length: 35181254.2 bp  

output as files

Sinv_bigB.1_cumCoord.list  
Sinv_bigB.1_diff.list  
Sinv_bigB.1_fused.cmap  
Sinv_bigB.1_selected.cmap  

what are these files?

• Sinv_bigB.1_cumCoord.list: coordinates of optical markers in the new, fused cmap
• Sinv_bigB.1_diff.list: temporary file listing the distances beween the optical markers in the cmaps. This is then used to calculate the new coordinates in the fused cmap
• Sinv_bigB.1_fused.cmap: contains the picked/flipped cmaps as fused, single new cmap (including the gaps) with the new ID and new coordinates
• Sinv_bigB.1_selected.cmap: contains the picked/flipped cmaps

create new whole_genome.cmap

run the above command for each chromosome/LG

for the unplaced contigs, simply run the same command (using some unique arbitrary value/string as new ID) and use the resulting $OUTPREFIX_selected.cmap to get all the unplaced contigs into a separate file

i=unplaced  
./cmap_pick_flip_merge.sh Sinv_bigB_all_unplaced_cmaps.lst 50000 $i Sinv_bigB.cmap Sinv_bigB_unplaced  

concatenate the cmaps (be aware of numerical sorting issues):

ls -1 Sinv_bigB.{1..9}_fused.cmap
ls -1 Sinv_bigB.{10..16}_fused.cmap  

cat Sinv_bigB.{1..9}_fused.cmap > Sinv_bigB_whole_genome_in_LGs.cmap  
cat Sinv_bigB.{10..16}_fused.cmap >> Sinv_bigB_whole_genome_in_LGs.cmap  

unplaced optical-contigs are in: Sinv_bigB_unplaced_selected.cmap (beware of cmap-contig-IDs which are overlapping with the new IDs in the *_fused.cmap