Problems using V-FAT for large DNA viruses

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Dan Depledge

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Dec 12, 2015, 3:16:14 AM12/12/15

to Broad Viral Tool Users

Hi,

I've been experimenting with using V-FAT to orient and merge de novo contigs to herpesvirus genomes. However, the alignment of the contigs only occurs in the first ~50kb of the genome (genome size is ~150 kp) so I suspect there are some bugs present. I have subsequently BLASTed all contigs against my reference sequence and these contigs do in fact map across the whole genome

V-FAT output

1 4441 contig_0 1-4444

4442 5084 contig_0 4445-5088

5085 5726 contig_10 644-1284

5727 5787 contig_0 5731-5791

5788 6095 contig_0 5792-6099

6096 6403 contig_10 1593-1897

6404 20604 contig_0 6408-20626

20605 20877 contig_0 20627-20905

20878 21150 contig_7 20878-21150

21151 21173 contig_7 21151-21173

21174 21196 contig_4 701-723

21197 23952 contig_4 724-3479

23953 26708 contig_6 2764-5519

26709 28415 contig_6 5520-7226

28416 30122 contig_4 7944-9648

30123 34037 contig_7 30123-34037

34038 38258 contig_7 34038-38258

38259 39208 950N

39209 40423 contig_10 1932-3148

40424 41036 contig_10 3210-3825

41037 43862 2826N

43863 53081 contig_1 9074-18292

BLAST output

NODE_17_length_1291_cov_66.5906_ID_851	397	966
NODE_21_length_546_cov_41.7292_ID_859	1024	1400
NODE_9_length_2256_cov_87.8687_ID_835	1496	2359
NODE_9_length_2256_cov_87.8687_ID_835	2417	2814
NODE_9_length_2256_cov_87.8687_ID_835	2846	3796
NODE_23_length_350_cov_73.8278_ID_863	3879	4225
NODE_11_length_2109_cov_68.5535_ID_839	4442	5814
NODE_11_length_2109_cov_68.5535_ID_839	5788	6403
NODE_15_length_1718_cov_73.5874_ID_847	6572	8157
NODE_25_length_275_cov_50.2929_ID_867	8235	8510
NODE_4_length_11427_cov_83.2741_ID_825	9203	20580
NODE_5_length_10795_cov_83.8694_ID_827	20605	31262
NODE_10_length_2166_cov_77.9943_ID_837	21370	21446
NODE_13_length_2014_cov_79.4254_ID_843	31355	33314
NODE_7_length_9463_cov_78.4296_ID_831	33299	42766
NODE_3_length_14268_cov_80.2911_ID_823	42749	56768
NODE_8_length_5697_cov_81.1498_ID_833	56776	62477
NODE_2_length_18292_cov_83.7743_ID_821	62404	71620
NODE_2_length_18292_cov_83.7743_ID_821	62404	71620
NODE_8_length_5697_cov_81.1498_ID_833	62474	62547
NODE_22_length_500_cov_43.0355_ID_861	71865	72353
NODE_12_length_2111_cov_64.2074_ID_841	72749	74223
NODE_12_length_2111_cov_64.2074_ID_841	74306	74784
NODE_1_length_42352_cov_78.8134_ID_819	74789	117153
NODE_5_length_10795_cov_83.8694_ID_827	95263	95381
NODE_25_length_275_cov_50.2929_ID_867	117864	118139
NODE_15_length_1718_cov_73.5874_ID_847	118217	119802
NODE_11_length_2109_cov_68.5535_ID_839	119971	120586
NODE_11_length_2109_cov_68.5535_ID_839	120560	121932
NODE_23_length_350_cov_73.8278_ID_863	122149	122495
NODE_9_length_2256_cov_87.8687_ID_835	122578	123528
NODE_9_length_2256_cov_87.8687_ID_835	123560	123957
NODE_9_length_2256_cov_87.8687_ID_835	124015	124878
NODE_21_length_546_cov_41.7292_ID_859	124974	125350
NODE_17_length_1291_cov_66.5906_ID_851	125408	125977
NODE_17_length_1291_cov_66.5906_ID_851	126406	126600
NODE_17_length_1291_cov_66.5906_ID_851	126685	126838
NODE_17_length_1291_cov_66.5906_ID_851	127119	127472
NODE_18_length_1120_cov_71.8476_ID_853	127587	128706
NODE_19_length_733_cov_48.4177_ID_855	129594	130319
NODE_16_length_1533_cov_73.2527_ID_849	130389	131920
NODE_10_length_2166_cov_77.9943_ID_837	132059	132428
NODE_10_length_2166_cov_77.9943_ID_837	132478	134236
NODE_6_length_9467_cov_79.7971_ID_829	134242	143723
NODE_14_length_1727_cov_88.957_ID_845	143836	145572
NODE_10_length_2166_cov_77.9943_ID_837	145583	145719
NODE_10_length_2166_cov_77.9943_ID_837	145769	146138
NODE_16_length_1533_cov_73.2527_ID_849	146277	147808
NODE_19_length_733_cov_48.4177_ID_855	147878	148603
NODE_18_length_1120_cov_71.8476_ID_853	149491	150610
NODE_17_length_1291_cov_66.5906_ID_851	150725	151078
NODE_17_length_1291_cov_66.5906_ID_851	151359	151512
NODE_17_length_1291_cov_66.5906_ID_851	151597	151791

(Note the contig names are different due to how V-FAT renames them during its operation)

Has anyone tried V-Fat with genomes larger than 50kb and if so, did you experience similar troubles and do you have any solutions?

Thanks,

Dan

Daniel Park

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Feb 1, 2016, 11:35:20 AM2/1/16

to Broad Viral Tool Users

Hi Dan,

I've also recently tried to use V-FAT on viruses from the herpes family and it fails to produce any output at all (empty output files) despite good coverage data going in. I'm currently attempting to replace it with something MUMmer-based, but it is still a work in progress and has not been merged in yet.