Minimap2: Visualizing MINIMAP2 Output

[tramaraj]

Dear Users:

I have used MINIMAP2 to generate alignments between two genome assemblies. I have a sorted and indexed BAM file. Is there a way to generate plots to visualize the whole genome alignments generated.

ThankS!

[lh3]

Ribbon?

CC @MariaNattestad

[lh3]

Another approach is to use minidot from miniasm. You need to output in the PAF format though like:

minimap2 -c -x??? asm1.fa asm2.fa > out.paf
minidot out.paf > out.eps && epstopdf out.eps

[tramaraj]

Thanks for the recommendations!

[dcopetti]

Hello,

I tried running the minidot step after the alignment:

minimap2 -c -x??? asm1.fa asm2.fa > out.paf
minidot out.paf > out.eps && epstopdf out.eps
```
I do

minimap2 -c -x asm10 ctg_0_index.mmi ctg_0h.fa >ctg_0h_aln10.paf
minidot ctg_0h_aln10.paf >ctg_0h_aln10.eps

and I always get an empty file, even though my two sequences have plenty of alignments:

000000F_001     39428   8       39424   +       000000F 6180273 927167  966619  36969   39547   60      tp:A:P  cm:i:6596       s1:i:36967      s2:i:1322       dv:f:0.0079
000000F_002     44614   8       44607   +       000000F 6180273 3271288 3315877 42537   44712   60      tp:A:P  cm:i:7532       s1:i:42535      s2:i:1711       dv:f:0.0064
000000F_004     23990   7       23987   +       000000F 6180273 2261722 2285734 23263   24036   60      tp:A:P  cm:i:4171       s1:i:23262      s2:i:2907       dv:f:0.0042
000000F_005     36512   6       36487   +       000000F 6180273 5541525 5578064 33122   36639   60      tp:A:P  cm:i:5718       s1:i:33118      s2:i:3527       dv:f:0.0117
000000F_006     28570   1       28565   +       000000F 6180273 3896202 3924778 27483   28626   60      tp:A:P  cm:i:4946       s1:i:27483      s2:i:2256       dv:f:0.0052
000000F_007     26896   0       26894   +       000000F 6180273 2642728 2669670 25279   26995   60      tp:A:P  cm:i:4486       s1:i:25276      s2:i:1728       dv:f:0.0074
000000F_008     40028   9       40027   +       000000F 6180273 3221714 3261720 38722   40099   60      tp:A:P  cm:i:7017       s1:i:38717      s2:i:1468       dv:f:0.0047
000000F_009     45506   2       45463   +       000000F 6180273 4175261 4220614 43534   45625   60      tp:A:P  cm:i:7877       s1:i:43496      s2:i:9037       dv:f:0.0054
000000F_010     42437   5       42435   +       000000F 6180273 1293859 1336369 39879   42577   60      tp:A:P  cm:i:7114       s1:i:39875      s2:i:4278       dv:f:0.0076
000000F_011     75565   2       75563   +       000000F 6180273 2548117 2623724 70867   75790   60      tp:A:P  cm:i:12569      s1:i:70864      s2:i:2429       dv:f:0.0081
000000F_012     20108   7       20099   +       000000F 6180273 5638323 5658463 19212   20165   60      tp:A:P  cm:i:3456       s1:i:19211      s2:i:3669       dv:f:0.0062
000000F_013     27753   3       27738   +       000000F 6180273 5145648 5173428 26245   27837   60      tp:A:P  cm:i:4662       s1:i:26244      s2:i:4249       dv:f:0.0076
000000F_014     54000   6       52576   +       000000F 6180273 496876  549432  48523   52711   60      tp:A:P  cm:i:8604       s1:i:48504      s2:i:4410       dv:f:0.0089
000000F_014     54000   51948   53246   +       000000F 6180273 547455  548760  467     1313    60      tp:A:P  cm:i:49 s1:i:462        s2:i:335        dv:f:0.1045
000000F_014     54000   52712   53693   +       000000F 6180273 4454182 4455148 83      981     60      tp:A:P  cm:i:7  s1:i:81 s2:i:0  dv:f:0.2204
000000F_015     42279   4       42267   +       000000F 6180273 3415861 3458071 39500   42370   60      tp:A:P  cm:i:7006       s1:i:39496      s2:i:4474       dv:f:0.0087
000000F_016     31014   7       31007   +       000000F 6180273 4415256 4446370 27775   31217   60      tp:A:P  cm:i:4764       s1:i:27758      s2:i:6869       dv:f:0.0132
000000F_017     27934   1       27929   +       000000F 6180273 3595275 3623173 25651   28021   60      tp:A:P  cm:i:4450       s1:i:25649      s2:i:1845       dv:f:0.0107
000000F_018     85837   0       85834   +       000000F 6180273 5580381 5666310 83321   86020   60      tp:A:P  cm:i:15132      s1:i:83311      s2:i:6301       dv:f:0.0039
000000F_019     73264   6       73261   +       000000F 6180273 422498  495569  68685   73365   60      tp:A:P  cm:i:12199      s1:i:68672      s2:i:6221       dv:f:0.0078
000000F_021     22793   20      22789   +       000000F 6180273 697544  720331  22159   22800   60      tp:A:P  cm:i:4028       s1:i:22159      s2:i:1229       dv:f:0.0033
000000F_020     51199   3       51194   +       000000F 6180273 2932234 2983406 48470   51340   60      tp:A:P  cm:i:8687       s1:i:48456      s2:i:3082       dv:f:0.0068
000000F_022     35833   5       35821   +       000000F 6180273 4024792 4060598 34060   35906   60      tp:A:P  cm:i:6113       s1:i:34056      s2:i:3024       dv:f:0.0067

where is the problem?
Thanks