how to select a prefect results

[shehongbing]

I assembly about 100X ONT (raw data) using NextDenovo. And my genome is about 1G.

when I used default parameter the result is following.

• /ifs1/User/shehongbing/soft/NextDenovo/bin/nextgraph -a 1 -f /ifs1/User/shehongbing/zhuang/next/merge/merge_01/03.ctg_graph/01.ctg_graph.input.seqs /ifs1/User/shehongbing/zhuang/next/merge/merge_01/03.ctg_graph/01.ctg_graph.input.ovls -o nextgraph.assembly.contig.fasta [INFO] 2019-12-30 02:54:05 Initialize graph and reading... [INFO] 2019-12-30 02:55:11 Initial Node(s): 175253, Edge(s): 2333852 [INFO] 2019-12-30 02:55:13 Depth stat, Ave: 74.823 Max: 149645.938 Repeat: 155.362 Nor:Ext: 254094:97640 [INFO] 2019-12-30 02:55:13 Outdegree stat, Ave: 13.449 Max: 26898.375 Repeat: 20.755 Nor:Ext: 340684:9823 [INFO] 2019-12-30 02:55:26 Chimeric node ratio: 0.930% (candidate: 1.353%) [INFO] 2019-12-30 02:55:40 Assembly done and outputting... [INFO] 2019-12-30 03:01:39 Assembly stat: Type Length (bp) Count (#) N10 116204120 1 N20 114308081 2 N30 107094691 3 N40 31652831 5 N50 7783900 12 N60 2368060 41 N70 1638194 97 N80 1054077 184 N90 683091 316

Min. 49014 - Max. 116204120 - Ave. 1775606 - Total 1099099761 619

also, I noticed that a max N50 using the random parameter is following.

• /ifs1/User/shehongbing/soft/NextDenovo/bin/nextgraph -a 0 -u 1 -f /ifs1/User/shehongbing/zhuang/next/merge/merge_01/03.ctg_graph/01.ctg_graph.input.seqs /ifs1/User/shehongbing/zhuang/next/merge/merge_01/03.ctg_graph/01.ctg_graph.input.ovls [INFO] 2019-12-30 02:55:38 Initialize graph and reading... [INFO] 2019-12-30 02:56:13 Initial Node(s): 98576, Edge(s): 747728 [INFO] 2019-12-30 02:56:13 Depth stat, Ave: 73.900 Max: 147799.938 Repeat: 152.905 Nor:Ext: 144616:54866 [INFO] 2019-12-30 02:56:13 Outdegree stat, Ave: 7.809 Max: 15618.035 Repeat: 12.303 Nor:Ext: 187703:9450 [INFO] 2019-12-30 02:56:16 Chimeric node ratio: 1.520% (candidate: 2.085%) [INFO] 2019-12-30 02:56:18 Assembly done and outputting... [INFO] 2019-12-30 02:56:18 Assembly stat: Type Length (bp) Count (#) N10 102599639 1 N20 79963541 3 N30 45136607 4 N40 33626804 7 N50 24232552 11 N60 10614944 17 N70 4181683 33 N80 2435309 65 N90 1002506 132

Min. 109350 - Max. 102599639 - Ave. 3141996 - Total 999154593 318

we could noticed that these two parameter seems the same except -u, but the N50 value is total different. So I wanna know which I could choose.

Thx

[moold]

If you do not have other data, such as Bionano data, Hic data, closely related genomes, etc., just select the assembly with default parameters (ctg_graph00 directoty), otherwise you can use these data to evaluate the assemblies and select the best quality genome basing the evaluation results.

[shehongbing]

在 2019年12月30日，下午12:56，Hu Jiang notifications@github.com 写道：

If you do not have other data, such as Bionano data, Hic data, closely related genomes, etc., just select the assembly with default parameters (ctg_graph00 directoty), otherwise you can use these data to evaluate the assemblies and select the best quality genome basing the evaluation results.

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Thank you