Quast Oly
Running QUAST to compare genome assembly.
!python /Applications/bioinfo/quast-4.5/quast.py \
-t 8 \
-o /Volumes/Alanine/wd/17-09-13/ \
/Users/sr320/git-repos/nb-2017/O_lurida/data/ol-canu-170623.fa \
/Volumes/web/halfshell/working-directory/17-09-10/ol-bgisoap-161129.fa \
/Volumes/web/halfshell/working-directory/17-09-10/ol-redundans-170608.fa
Interactive results available here
including plain text stats
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).
Suggestion: assemblies ol-bgisoap-161129, ol-redundans-170608 contain continuous fragments of N's of length >= 10 bp. You may consider rerunning QUAST using --scaffolds (-s) option!
Assembly ol-canu-170623 ol-bgisoap-161129 ol-redundans-170608
# contigs (>= 0 bp) 3388 765755 300593
# contigs (>= 1000 bp) 3388 184804 137301
# contigs (>= 5000 bp) 3338 33792 24009
# contigs (>= 10000 bp) 2671 8733 6254
# contigs (>= 25000 bp) 121 553 586
# contigs (>= 50000 bp) 3 21 36
Total length (>= 0 bp) 46364927 776306190 546928670
Total length (>= 1000 bp) 46364927 642346712 476206320
Total length (>= 5000 bp) 46187705 302087694 220366692
Total length (>= 10000 bp) 40439853 131223850 99646272
Total length (>= 25000 bp) 3707809 17851807 19574809
Total length (>= 50000 bp) 174759 1283294 2106424
# contigs 3388 259186 188612
Largest contig 61211 130073 78788
Total length 46364927 697528655 513841258
GC (%) 36.53 35.83 35.90
N50 14126 4204 4175
N75 11429 2078 2103
L50 1230 43989 32022
L75 2145 103370 75613
# N's per 100 kbp 0.00 19149.50 1019.31
Written on September 15, 2017