Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

I think trouble was solved #13

Open
wants to merge 5 commits into
base: master
Choose a base branch
from
Open

I think trouble was solved #13

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
4941ab5
Add no-hybrid long-read assembly
natir Oct 14, 2018
bf715d4
Merge branch 'master' of github.com:hackseq/modular-assembly-hs18
natir Oct 14, 2018
d1062ef
Correct error in miniasm report
natir Oct 14, 2018
b179423
Fixed error in quast run
natir Oct 14, 2018
c0174d9
Fix error in quast run twice
natir Oct 14, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions assembly_stats/canu.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length Estimated reference length GC (%) N50 NG50 N75 NG75 L50 LG50 L75 LG75 # N's per 100 kbp
Canu 10 10 10 5 2 2 189520 189520 189520 145564 105666 105666 10 55538 189520 229883 43.81 50128 14962 10429 8915 2 3 5 8 0.00
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length Reference length GC (%) Reference GC (%) N50 NG50 N75 NG75 L50 LG50 L75 LG75 # misassemblies # misassembled contigs Misassembled contigs length # local misassemblies # scaffold gap size misassemblies # unaligned mis. contigs # unaligned contigs Unaligned length Genome fraction (%) Duplication ratio # N's per 100 kbp # mismatches per 100 kbp # indels per 100 kbp Largest alignment Total aligned length NA50 NGA50 NA75 NGA75 LA50 LGA50 LA75 LGA75
Canu 10 10 10 5 2 2 189520 189520 189520 145564 105666 105666 10 55538 189520 229880 43.81 44.99 50128 14962 10429 8915 2 3 5 8 6 4 130535 0 0 0 1 + 0 part 6943 68.321 1.162 0.00 152.81 965.90 32674 182565 22858 14507 8944 4648 4 5 8 12
4 changes: 2 additions & 2 deletions assembly_stats/miniasm.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length Estimated reference length GC (%) N50 NG50 N75 NG75 L50 LG50 L75 LG75 # N's per 100 kbp
Miniasm 7 7 7 5 3 1 192885 192885 192885 178413 139255 74073 7 74073 192885 229883 44.86 34878 30304 23341 15817 2 3 4 5 0.00
Assembly # contigs (>= 0 bp) # contigs (>= 1000 bp) # contigs (>= 5000 bp) # contigs (>= 10000 bp) # contigs (>= 25000 bp) # contigs (>= 50000 bp) Total length (>= 0 bp) Total length (>= 1000 bp) Total length (>= 5000 bp) Total length (>= 10000 bp) Total length (>= 25000 bp) Total length (>= 50000 bp) # contigs Largest contig Total length Reference length GC (%) Reference GC (%) N50 NG50 N75 NG75 L50 LG50 L75 LG75 # unaligned contigs Unaligned length # N's per 100 kbp NGA50
Miniasm 7 7 7 5 3 1 192885 192885 192885 178413 139255 74073 7 74073 192885 229880 44.86 44.99 34878 30304 23341 15817 2 3 4 5 7 + 0 part 192885 0.00 -