Question: velvet assembly problem with parameters
0
ilario.ferrocino • 0 wrote:
Hi there im try to do assembly with velvet on my metagenomic illumina single end sequence.
I'had try to use different kmer value but i have bad results like this:
How i can fix it??
| parameters -short | sample name | total number contigs | total contig length | largest contig length | mean/median contig length | N50 (bp) |
| assembly kmer 53 e ins 300 | 09.TO | 189,412 | 146,667,097 | 54,723 | 774/493 | 914 |
| assembly kmer 63 e ins 300 | 09.TO | 178,173 | 132,535,391 | 85,044 | 744/470 | 832 |
| assembly kmer 82 e ins 300 | 09.TO | 146,108 | 103,053,100 | 177,456 | 705/436 | 746 |
| assembly kmer 77 e ins 300 | 09.TO | 155,024 | 110,414,760 | 151,465 | 712/442 | 756 |
| assembly kmer 60 e ins 300 | 09.TO | 182,064 | 138,638,656 | 63,991 | 761/478 | 873 |
| assembly kmer 50 e ins 300 | 09.TO | 194.84 | 152,368,820 | 51,381 | 782/501 | 932 |
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modified 5.1 years ago
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dago • 2.6k
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5.1 years ago by
ilario.ferrocino • 0
How did you conclude these results are bad? How do you think better results should look like? These inputs will help set some context.