Assembly analysis

Assessment of genome assemblies through various evaluation methods

Motivation

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.

Results

QUAST vs. CHM13 draft v0.7

	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

Run commands

Shasta run 2 - Assembly performed using Shasta commit 8bb7d52d9f8622a8dee8c3fcfb58e4f4cd1ac9f8

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 - Analysis performed by Marina Haukness (UC Santa Cruz) using quast-5.0.2

quast-5.0.2/quast-lg.py --threads 128 -r ../chm13.draft_v0.7.fasta --large --min-identity 80 --fragmented Assembly.fasta