Assessment of genome assemblies through various evaluation methods
The CHM13 data and analyses from the Telomere-to-Telomere consortium (T2T) contain BAC analyses for the Canu, Flye, and Shasta assemblies. Here we add QUAST analysis, followed by the table, for the same.
| canu.contigs | flye.contigs | shasta.run2 | |
|---|---|---|---|
| # contigs | 1223 | 472 | 297 |
| Largest contig | 139909728 | 132009996 | 130803838 |
| Total length | 2991947723 | 2920201070 | 2823384269 |
| # misassemblies | 6396 | 3230 | 187 |
| # misassembled contigs | 875 | 193 | 78 |
| Misassembled contigs length | 2458710426 | 2440399207 | 1351075153 |
| # local misassemblies | 1164 | 981 | 129 |
| # possible TEs | 160 | 96 | 14 |
| # unaligned mis. contigs | 73 | 17 | 0 |
| # unaligned contigs | 168 + 248 part | 8 + 135 part | 0 + 37 part |
| Unaligned length | 30076945 | 14583673 | 393547 |
| Genome fraction (%) | 98.391 | 97.392 | 96.149 |
| Duplication ratio | 1.027 | 1.018 | 1.002 |
| # mismatches per 100 kbp | 77.26 | 74.04 | 15.56 |
| # indels per 100 kbp | 327.08 | 447.97 | 141.25 |
| Largest alignment | 104447985 | 111814657 | 111679369 |
| Total aligned length | 2943726417 | 2894073152 | 2821352191 |
| N50 | 77964612 | 70319350 | 58111632 |
| NG50 | 77964612 | 70319350 | 58088067 |
| L50 | 15 | 16 | 17 |
| LG50 | 15 | 16 | 18 |
| NA50 | 47440498 | 46858921 | 47392260 |
| NGA50 | 47440498 | 46546094 | 44539326 |
| LA50 | 21 | 19 | 19 |
| LGA50 | 21 | 20 | 20 |
nohup bin/shastaDynamic --input rel3.fasta --Reads.minReadLength 50000 --MinHash.minBucketSize 10 --MinHash.maxBucketSize 40 --MinHash.minFrequency 10 --MinHash.minHashIterationCount 0 --MinHash.alignmentCandidatesPerRead 10 --Align.minAlignedMarkerCount 400 --Align.minAlignedFraction 0.4 --Align.sameChannelReadAlignment.suppressDeltaThreshold 10 --Assembly.consensusCaller Bayesian:guppy-3.0.5-a --memoryMode filesystem --memoryBacking 2M --assemblyDirectory run2 1>run2.stdout 2>&1 &
quast-5.0.2/quast-lg.py --threads 128 -r ../chm13.draft_v0.7.fasta --large --min-identity 80 --fragmented Assembly.fasta