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| The results... |
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| The results... |
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Final graph has 9748 nodes and n50 of 191, max 1427, total 1865207, using 281499/2314900 reads |
Median coverage depth = 2.657895
Final graph has 9748 nodes and n50 of 191, max 1427, total 1865207, using 281499/2314900 reads
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| title | Set with one group of reads at 50 coverage |
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Final graph has 271 nodes and n50 of 127086, max 397281, total 4555586, using 1464199/2314900 reads |
Median coverage depth = 11.131337
Final graph has 265 nodes and n50 of 127102, max 397974, total 4558511, using 1464201/2314900 reads
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| title | Set with 2 groups of reads both at 25 coverage each |
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Final graph has 203 nodes and n50 of 698134, max 1032531, total 4585717, using 1465818/2314900 reads |
Median coverage depth = 11.109244
Final graph has 203 nodes and n50 of 698134, max 1032531, total 4585717, using 1465818/2314900 reads
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| title | Set with 3 groups of reads all at 20 coverage each |
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Final graph has 202 nodes and n50 of 698626, max 1139610, total 4602729, using 1758595/2777880 reads |
Median coverage depth = 13.353287
Final graph has 202 nodes and n50 of 698626, max 1139610, total 4602729, using 1758595/2777880 reads
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With better read pairs that link more distant locations in the genome, there are fewer contigs, and contigs are are longer, giving us a more complete picture of linkage across the genome.
The complete E. coli genome is about 4.6 Mb. Why weren't we able to assemble it, even with this "perfect" data?
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| One possibility Possibilities... One possibility.. |
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| Possibilities... |
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- Sometimes errors in reads lead to dead-ends in the graphs that are trimmed when they should not be.
- There are 7 nearly identical ribosomal RNA operons in E. coli spaced throughout the chromosome. Since each is >3000 bases, contigs cannot be connected across them using this data.
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More assembly statistics: contig_stats.pl
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