From 1c658636d4db12b92a0a4a9cc8c2329e71fb2fb3 Mon Sep 17 00:00:00 2001 From: Niko <nikolaos.papadopoulos@univie.ac.at> Date: Tue, 19 Nov 2024 22:30:31 +0100 Subject: [PATCH] added genome assembly progress --- 02-scaffolding/README.md | 51 +++++++++++++++++++++++++++++++++++++++- 1 file changed, 50 insertions(+), 1 deletion(-) diff --git a/02-scaffolding/README.md b/02-scaffolding/README.md index 00b5672..9d9b191 100644 --- a/02-scaffolding/README.md +++ b/02-scaffolding/README.md @@ -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. \ No newline at end of file +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> \ No newline at end of file -- GitLab