生物信息学

20220324_比较基因组结果可视化

Song Wei 2023年3月12日 05:43

152

20220324_比较基因组结果可视化

(1)首先使用minimap2软件对两个基因组进行比较

(base) root@dell-server:/home/newdisk_dell_6/wilson/lizi/lizi-flye-2021-10-11-11-04-09_result-1/collinearity_result/f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.GCA_014863905-ok/pafr_result# ls -lhtr
总用量 531M
-rw-r--r-- 1 root root 262M 3月  24 18:11 GCA_014863905-ok.fasta
-rw-r--r-- 1 root root 270M 3月  24 18:18 f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.fasta


(base) root@dell-server:/home/newdisk_dell_6/wilson/lizi/lizi-flye-2021-10-11-11-04-09_result-1/collinearity_result/f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.GCA_014863905-ok/pafr_result#  minimap2  GCA_014863905-ok.fasta  f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.fasta   -t 60 -c > GCA_014863905-ok-query.paf
[M::mm_idx_gen::6.965*1.62] collected minimizers
[M::mm_idx_gen::8.495*3.19] sorted minimizers
[M::main::8.495*3.19] loaded/built the index for 8 target sequence(s)
[M::mm_mapopt_update::8.934*3.09] mid_occ = 348
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 8
[M::mm_idx_stat::9.162*3.03] distinct minimizers: 22464014 (65.44% are singletons); average occurrences: 2.297; average spacing: 5.319
[M::worker_pipeline::974.509*4.88] mapped 8 sequences
[M::main] Version: 2.17-r941
[M::main] CMD: minimap2 -t 60 -c GCA_014863905-ok.fasta f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.fasta
[M::main] Real time: 974.653 sec; CPU: 4753.080 sec; Peak RSS: 33.207 GB


(base) dell@dell-server:/home/newdisk_dell_6/wilson/lizi/lizi-flye-2021-10-11-11-04-09_result-1/collinearity_result/f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.GCA_014863905-ok/pafr_result$ ls -lhtr
总用量 538M
-rw-r--r-- 1 root root 262M 3月  24 18:11 GCA_014863905-ok.fasta
-rw-r--r-- 1 root root 270M 3月  24 18:18 f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.fasta
-rw-r--r-- 1 root root 6.4M 3月  24 18:45 GCA_014863905-ok-query.paf
(base) dell@dell-server:/home/newdisk_dell_6/wilson/lizi/lizi-flye-2021-10-11-11-04-09_result-1/collinearity_result/f1-hicpro-allhic-ok-chr1-chr2-chr4-chr7-ReverseComplementary.GCA_014863905-ok/pafr_result$ less -S GCA_014863905-ok-query.paf
chr1    54688106        45479452        46602367        +       CM026527.1_chromosome_1 54530904        45840431        46960494        1118541 1124349 60  NM:i:5808        ms:i:2224678    AS:i:2229792    nn:i:0  tp:A:P  cm:i:202046     s1:i:1091528    s2:i:9234       de:f:0.0002     rl:i:4241097    cg:Z:16929M3I7038M1D2837M2I31753M1D807M6I14631M2D22M1I41221M3I3735M5I33114M1D3519M2D25850M16I816M3I24406M2I256M1I1895M2I21963M2I29089M1D1162M1D10023M4I13245M5I13620M2I34862M358D8767M1D3233M101D4252M2I4139M2I4302M2D75M17I12030M2I16990M1I301M2I2554M11D1997M8I8157M2D77M2I16540M1I38M1I66M1I13539M31I12469M2I12492M1I119M1I27496M10I136M1D3753M2I5M1D1804M2I26106M1I7895M25I105M23I27070M4I1350M196D306M2I14M4I455M1I5030M2D498M3I1152M3I9852M2140I7M1I3M1I3M2I7M1I4M8I3M1I9M1D5M2I2M2I5M2I5M2I6M1D10M388I19M1I1M1413I632M2I5986M2I485M2I122M1I4731M1I13137M2I10896M1D9473M6I2891M1D655M1I5M21I12M21D5M1D1431M2D7357M1D304M1I1193M2D5729M2I16668M1D16809M1D10991M4D24909M4I33315M4I5349M4I44590M3I4517M3I8108M1I11362M1D5563M2I8424M2D324M3I24890M2I809M1I10943M1I16130M2I6456M2I30673M2I6934M1I22187M2D10812M467D342M190D2684M2I50901M2D22193M1I7607M2I84M2D1316M8I1925M2D1458M4I8051M1I6810M5I8811M1I6413M2D23210M1I321M1I1525M1D1514M2I10087M1D5M1D73M1D154M1D100M1I40M3I206M1D980M1D199M1D788M1D478M18D430M1D478M1D220M1D40M1D136M1D88M1D838M3I768M7D2017M2D1463M1D23M
chr1    54688106        5464032 6376621 +       CM026527.1_chromosome_1 54530904        5800728 6714269 912053  913887  60      NM:i:1834       ms:i:1819502AS:i:1820601     nn:i:0  tp:A:P  cm:i:168526     s1:i:904809     s2:i:8492       de:f:0.0004     rl:i:4241097    cg:Z:11892M1I13753M6I8295M2D29137M1I7362M1D1499M1D1928M6I18M1D306M247D2164M5I8507M2D6310M2I15513M1D2501M1D1985M2D1751M2D8509M1I12464M1I2494M18D10397M3I18414M2D8715M1I10247M4I20736M1D24M2I33123M8I887M1D14868M2I2488M2D1898M12D9435M2D25060M1I6978M1I4093M2I32801M1I16204M4I7M2D56571M67I8837M2I52635M4D21246M6I4419M2D77643M2I13189M1D327M1I2005M1I12008M2I10481M4D37271M1I1781M1D3765M2I14742M2D27524M2I3795M2D2789M3I12681M2D16982M1I2347M2I19269M12I4403M4I3862M1I806M2I1480M137D65M3I207M14D71M26D11M1D189M1I779M2D1204M1I934M9I2862M1D994M3I504M1D825M174D1329M7I34545M1I144M4I17135M5I484M4I36743M1D616M2D1230M1D133M3I1610M1D434M1D11M1D2928M1D962M2I55M6I1972M3I109M1I1031M3I5263M1I559M1D319M1D1865M1D100M12I619M1D4M4D2M1D1M1D7M471D2154M1D2527M1D209M1D842M1I46M1D243M1D9M1D139M2D417M20D254M1D280M15I1363M1D624M1D1603M1D126M1D30M1D362M1D29M1D8M1D5M1D5M1D54M1D440M1D2558M1I1170M19D1580M1D92M1I448M1D208M2D340M1D1524M3I451M1I610M1D599M4I4172M1D68M1D825M1I717M1I475M86I84M67D77M
chr1    54688106        3622925 4388208 +       CM026527.1_chromosome_1 54530904        3777215 4542866 764912  765911  60      NM:i:999        ms:i:1527296AS:i:1527924     nn:i:0  tp:A:P  cm:i:139084     s1:i:747361     s2:i:7904       de:f:0.0002     rl:i:4241097    cg:Z:23M1I132M7D9M2D5M3I11851M2I16643M2I2216M2D19999M4I2702M1D38876M6I123M1I1130M6I12545M2D4375M2I1924M1I1940M7I2010M1D48755M2I5M1D9283M1D22974M2I9239M1I1003M2I3103M10I2067M1D8M1I3M1I8820M1I14M1I52M2I6934M1I2088M4I15797M3I47116M1D5M3I1455M1I23M12D514M1I957M1D263M105I267M2I21M2D1484M1I524M1D167M2I1018M286D1835M8I21130M1I1718M2I18601M1I45299M2D23177M1D12029M2I9400M3D93187M1I10972M2I4687M1I7172M1I7456M2I4513M1I61952M4I15632M1D10575M2D39369M1D58805M285D270M1D10M2I2452M1I413M9I843M32I863M5I362M1D998M2I1083M1I2585M1I3861M1D2607M9D705M
chr1    54688106        14797804        15526370        +       CM026527.1_chromosome_1 54530904        15715416        16447866        727170  733568  60  NM:i:6398        ms:i:1439816    AS:i:1444956    nn:i:0  tp:A:P  cm:i:132017     s1:i:713866     s2:i:7593       de:f:0.0008     rl:i:4241097    cg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
chr1    54688106        52338835        53043662        +       CM026527.1_chromosome_1 54530904        52256595        52955697        698193  705422  60  NM:i:7229        ms:i:1380480    AS:i:1386647    nn:i:0  tp:A:P  cm:i:128066     s1:i:688424     s2:i:624        de:f:0.0007     zd:i:2  rl:i:4241097    cg:Z:595M1I4918M1I1179M1D26M1I6M4D501M52D337M1D23M1D977M1D127M1I3139M1D1071M1D623M1D29M1D413M1D1928M1D31M1I15M1I1684M2D4382M1D4M1I6048M1D13962M2D1720M1D921M2I54M2I4642M2I11418M2I20040M43I32926M2D33685M2I71551M2D2190M2I19248M6I12829M1D29209M4I82M1I12958M2I34229M2D125M3D131M4I24953M2I4449M1I1230M2I1237M2I307M2D9120M5I40562M8I2466M3I12389M6I15558M1I23594M3D43314M1I44116M1D78M1D555M1D1355M4D7M30D10702M3I11106M1D1843M1D3127M1I10709M14D1293M2I60M286D403M2I2318M3I935M2D21M7D505M3D1M1D576M1D930M3D103M1D101M2I42M2D328M3I456M1I560M1I1550M2D1096M1D281M14D5M2D3M2D26M3D340M1I9M1I208M1D318M2D550M1I780M1I254M1D5604M2D3531M2I528M13D715M3I825M1I169M1I817M2I334M4I289M2I242M1I320M1I176M2I333M1I491M1I1159M3I316M1D494M1I104M3I389M1D231M1D346M1D77M5I48M1D235M1D394M4I64M8D24M1I191M161I32M7I9M352I86M1I230M1D161M1I156M5I60M1D448M1333I477M2470I12M4I30M353I134M1D148M1D19M2I312M1D19M4I25M1D146M7I92M2D230M2D207M2I8M1D103M3I55M1I98M2D7M1D24M4I121M493I197M1I260M1D738M1D653M4I478M337I259M2I1141M1I310M1D192M1I293M1I591M4I10550M2I1736M1I2799M2D10M1D6531M1D1592M2D1965M1D3154M12D108M469I113M2D3M10D542M1D551M3I759M1D778M1I1M1I159M1D4620M1D474M1D247M2D93M2D375M1D1716M1I3870M1D2131M22I217M4I1014M1I1647M3I364M3I3309M28D1978M2I533M1D695M3I2454M1D865M1D610M1D880M3I10M7I7M10I36M2I26M1I19M38I233M4I834M6I2264M1I1234M8I589M
chr1    54688106        12816554        13487139        +       CM026527.1_chromosome_1 54530904        13743151        14418721        669615  676137  60  NM:i:6522        ms:i:1323944    AS:i:1328880    nn:i:0  tp:A:P  cm:i:122789     s1:i:661559     s2:i:8388       de:f:0.0011     rl:i:4241097    cg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
chr1    54688106        15526353        16149161        +       CM026527.1_chromosome_1 54530904        16457517        17080531        622496  623289  60  NM:i:793 ms:i:1243080    AS:i:1243613    nn:i:0  tp:A:P  cm:i:111043     s1:i:598868     s2:i:8111       de:f:0.0002     rl:i:4241097    cg:Z:7M1I3M1I6843M1I29570M1D33137M8I33942M2I16386M12D10023M1I39264M1D6915M1I1865M3I2M1D3M1D2M1D11M1I8M1I4M1I2M3D27294M2D17502M2D261M4I92M1I16948M6I9148M1D12447M1D6883M2I11947M2D5398M2I12681M2I10465M1I25613M1D52933M1I10847M8I3733M438D1062M1D498M1D1989M5I1510M1D14816M4I4259M4I4728M2I11856M2I2354M1I14989M86I12661M2D7630M1D983M2I30830M3I8321M8I8148M1I815M4I6595M4I21986M5I2714M4D10559M2D11243M3I928M8I5129M69I5377M1I575M1I8M2D1347M13I13652M1I12792M
chr1    54688106        27984973        28568292        +       CM026527.1_chromosome_1 54530904        28686302        29271802        581452  586722  60  NM:i:5270        ms:i:1149694    AS:i:1153075    nn:i:0  tp:A:P  cm:i:92017      s1:i:510410     s2:i:10354      de:f:0.0017     rl:i:4241097    cg:Z:503M2I25M2I163M1D2M28I591M1D10M2I114M3I19M8I566M3I394M2I12M5I7M1D44M3I47M2I2M1I11M4I3M3I38M1I242M5I14M1I266M1I49M2I152M1D5M4I251M2I8M1I876M12I533M44D500M4I1499M3D28M3I99M11I367M1D4M4I484M1I18M1I684M1D279M7I39M2I493M1I507M4I1990M1I501M1I610M1D887M1D4M2I49M1D61M2D69M1D4M4I121M1I115M4D5M10D22M3D12M1D4M1I8M2D5M3D4M1D3M1I3M1I1M2I5M1D1M3D8M4D3M1I9M3D3M3D2M1I5M4D14M2I815M1I26M53I249M3I428M18I78M3I498M1I497M2D317M1D6M2I2M2I10M2I40M4I627M4I1295M1I6894M4I27985M18I790M4I1864M113I609M1D284M1D6M1D1M1D20M202I837M2I1205M1D422M5I279M1I1498M1D500M1D496M1D2M2D6367M14I14302M1D627M2I44M1I6M1I778M5I536M2I2590M1I1270M1I74M1D18654M1I686M1D958M1D120M1D1269M2I2635M1D203M1I372M1D1683M1D713M1D397M1I509M1D594M1D502M1D1537M1I1686M1D2358M1D1M2D521M1D29030M5I2969M1I1500M141D311M1D48M1I997M3I6M1I994M1I743M1I1258M400D609M4I323M2I175M2I705M3I219M2I67M1I6M4I72M1I378M5D3M39D501M6D3477M26D489M1I507M1I1M1I67M11I238M4I990M1I4696M1D1496M1D135M1I986M27I380M1D31M1D13M2I19M1D38M2I14M1I11M2D805M1D264M295D2293M3I2206M126D375M3I1M1I1M1I498M3I499M1D492M4D5M4D3M1D499M2I489M2D947M1I53M1D1008M3I491M1D1499M1D500M1I201M1I302M3I28M3D279M2I2M10I674M2D510M3I77M3D418M1I621M1I129M2D146M102D5531M1D2619M1I1831M1I6437M1D1713M1D233M3I44M1I14M3I1073M1D2381M2I13M8I8306M3I6640M2I4634M1I2401M1I2124M1D507M3I1492M1D126M2I153M5I21M1I44M2D156M1I33M3I9M3I5M2I47M2I795M1I47M6I24M1D7M1D3M4D12M1D9M1I4M9I2M1I35M5D599M6I44M1I22M6I288M1D497M4I121M4I879M2D823M1D292M1I8M378D2112M2I2794M12D7077M3D496M2I387M1D41M1D9M1D1M2I1096M1I303M1I161M1I1999M1D500M2I492M1I4M2D370M1D1137M2I1784M3I206M1D872M1D34M1D16M1D157M420D437M4I4711M23I37495M12I6828M1I251M1D4746M1I9077M2I10452M2D11501M5I4M2I4M3I1M1I2M3I571M2I6634M2I1750M13I30M1I2M2I5420M1I21916M1I774M2I3425M1I32889M1I9133M1I5250M1I2908M2I9068M1I92M11I150M10I68M20I28M1D18M19I22M2D37M5I116M1I60M3I7M25I632M1I1001M2I502M1D501M2I495M1D501M2I495M1I4M2D506M2I257M1D1736M5I996M1D503M3I25504M1I6995M390D995M5I1118M3I994M2I1503M1D999M3I497M1D1070M128I739M1I34992M1I10878M8I18319M367D716M1D2919M3I178M1D306M1D11M1D2986M8I514M1I1503M1I249M1D273M474D2822M
chr1    54688106        4426364 5027424 +       CM026527.1_chromosome_1 54530904        4617815 5213415 588911  607002  60      NM:i:18091      ms:i:1138714AS:i:1154762     nn:i:0  tp:A:P  cm:i:106269     s1:i:576234     s2:i:4492       de:f:0.0019     rl:i:4241097    cg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
chr1    54688106        26925456        27497172        +       CM026527.1_chromosome_1 54530904        27294316        27867323        570936  573469  60  NM:i:2533        ms:i:1135098    AS:i:1136666    nn:i:0  tp:A:P  cm:i:98518      s1:i:536841     s2:i:164195     de:f:0.0010     rl:i:4241097    cg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

（2）pafr软件对基因组比较结果进行可视化

library(BiocManager)
BiocManager::install("pafr")
library(pafr)
library(tidyverse)
library(ggplot2)

################################################
fungi.paf.1<-read_paf("GCA_014863905-ok-query.paf")
fungi.paf.1 %>% as.data.frame() %>% head()
fungi.paf.2<-read_paf("GCA_014863905-ok-query.paf",include_tags = FALSE)
fungi.paf.2 %>% as.data.frame() %>% head()
dotplot(fungi.paf.2)


plot_coverage(fungi.paf.2) -> p1
p1
plot_coverage(fungi.paf.2,fill='qname') -> p2
p2
plot_coverage(fungi.paf.2,fill='qname')+
  scale_fill_brewer(palette = "Set1") -> p3
p3