Assembly evaluation - linnasp/GenomeAnalysis_VT2026_Lab GitHub Wiki

Quast

All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs).

Assembly assembly pilon
hastag contigs (>= 0 bp) 43 43
hastag contigs (>= 1000 bp) 43 43
hastag contigs (>= 5000 bp) 36 36
hastag contigs (>= 10000 bp) 34 35
hastag contigs (>= 25000 bp) 25 25
hastag contigs (>= 50000 bp) 18 18
Total length (>= 0 bp) 16823629 16854129 Total length (>= 1000 bp) 16823629 16854129 Total length (>= 5000 bp) 16799781 16830248 Total length (>= 10000 bp) 16780217 16820662 Total length (>= 25000 bp) 16625363 16655617 Total length (>= 50000 bp) 16373424 16403140 hastag contigs 43 43
Largest contig 5054216 5064332
Total length 16823629 16854129 GC (%) 42.06 41.89
N50 2073827 2078026
N90 366595 367378
auN 2614920.7 2620103.4 L50 3 3
L90 10 10
hastag N's per 100 kbp 0.00 0.00

BUSCO

C:9.3%[S:9.2%,D:0.1%],F:0.4%,M:90.3%,n:1614
150 Complete BUSCOs (C)
148 Complete and single-copy BUSCOs (S)
2 Complete and duplicated BUSCOs (D)
6 Fragmented BUSCOs (F)
1458 Missing BUSCOs (M)
1614 Total BUSCO groups searched

Assembly Statistics: 43 Number of scaffolds 43 Number of contigs 16854129 Total length 0.000% Percent gaps 2 MB Scaffold N50 2 MB Contigs N50

Dependencies and versions: hmmsearch: 3.4 bbtools: None makeblastdb: 2.16.0+ tblastn: 2.16.0+ augustus: 3.5.0 gff2gbSmallDNA.pl: None new_species.pl: None etraining: None python: sys.version_info(major=3, minor=12, micro=3, releaselevel='final', serial=0) busco: 5.8.2

16/191.61x100=8.350