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Commit 1c658636 authored by Niko (Nikolaos) Papadopoulos's avatar Niko (Nikolaos) Papadopoulos
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added genome assembly progress

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02-scaffolding/README.md
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......@@ -20,4 +20,53 @@ We used the same evaluation scripts as during the assembly procedure to evaluate
scaffolded assemblies. We decided in favor of the `yahs` assembly, as it had higher contiguity and
better BUSCO scores. Following that, the assembly and omniC map were manually edited in
[juicebox](https://github.com/aidenlab/Juicebox) to correct clear chromosome rearrangements and
smaller misassemblies. The corrected scaffold was exported in FASTA form and used from here on out.
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smaller misassemblies. The corrected scaffold was exported in FASTA form and used from here on out.
## Genome assembly progress
<details>
<summary>Click to expand</summary>
Starting out from the `flye` assembly, progressing to scaffolding with yahs, manual curation with
juicebox (and removal of obvious contaminant scaffolds), ending with the GAP `sort_scaffolds`
pipeline.
| Assembly | flye | flye | flye + jb | rd2 + decont | BRAKER | ISO-seq + BRAKER |
|----------------------------|-------------|-------------|-------------|---------------|--------|------------------|
| scaffolder | - | yahs | yahs + me | yahs + me | - | - |
| # contigs (>= 0 bp) | 10,856 | 12,371 | 10,767 | 10,257 | - | - |
| # contigs (>= 1000 bp) | 13,520 | 9,707 | 8,199 | 7,689 | - | - |
| **# contigs (>= 5000 bp)** | **3,429** | **2,280** | **1,332** | **790** | - | - |
| # contigs (>= 10000 bp) | 2,677 | 1,528 | 749 | 510 | - | - |
| # contigs (>= 25000 bp) | 1,824 | 725 | 310 | 220 | - | - |
| # contigs (>= 50000 bp) | 1,321 | 381 | 140 | 108 | - | - |
| Total length (>= 0 bp) | 529,880,842 | 530,110,642 | 470,215,199 | 471,606,659 | - | - |
| Total length (>= 1000 bp) | 528,047,687 | 528,277,487 | 468,450,049 | 469,841,509 | - | - |
| Total length (>= 5000 bp) | 508,723,655 | 508,953,455 | 450,696,092 | 452,022,552 | - | - |
| Total length (>= 10000 bp) | 503,406,950 | 503,636,750 | 446,677,803 | 450,081,153 | - | - |
| Total length (>= 25000 bp) | 489,576,998 | 490,943,099 | 439,890,306 | 445,538,587 | - | - |
| Total length (>= 50000 bp) | 471,872,883 | 479,062,479 | 434,157,830 | 441,710,284 | - | - |
| **#contigs** | **13,427** | **12,278** | **10,675** | **10,165** | - | - |
| Largest contig | 4,458,759 | 18,159,430 | 13,781,389 | 14,198,558 | - | - |
| Total length | 529,844,325 | 530,074,125 | 470,179,169 | 471,570,629 | - | - |
| GC (%) | 40.21 | 40.21 | 39.67 | 39.66 | - | - |
| N50 | 522,825 | 7,393,989 | 7,715,281 | 7,968,359 | - | - |
| N90 | 42,521 | 56,483 | 3,832,569 | 4,275,246 | - | - |
| auN | 743,185.5 | 7,692,823.7 | 7,600,557.7 | 7,994,033.9 | - | - |
| L50 | 277 | 24 | 24 | 23 | - | - |
| L90 | 1,430 | 344 | 56 | 54 | - | - |
| # N's per 100 kbp | 0.00 | 43.35 | 28.56 | 42.98 | - | - |
|||||||
| Approx. runtime (CPUs) | 21h (30) | 7min(1) | (a week?) | - | 17h | - |
|||||||
| BUSCO metazoa complete | 94.2% | 96.7% | 96.7% | - | 96.0% | 95.7% (90.3%) |
| BUSCO metazoa single | 87.8% | 91.0% | 91.0% | - | 79.2% | 40.1% (87.1%) |
| BUSCO metazoa duplicated | 6.4% | 5.7% | 5.7% | - | 16.8% | 55.6% (3.2%) |
| BUSCO metazoa fragmented | 3.6% | 1.6% | 1.6% | - | 0.5% | 1.3% (1.5%) |
| BUSCO metazoa missing | 2.2% | 1.7% | 1.7% | - | 3.5% | 3.0% (8.2%) |
For Iso-seq ft. BRAKER the numbers in parentheses are the BUSCO results after keeping one "best"
isoform per locus (rules: longest complete CDS > complete CDS > longest CDS).
</details>
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