From 4941ab5795d3ca2cebb0eb30be4b8db14272c9e9 Mon Sep 17 00:00:00 2001 From: Marijon Pierre Date: Sun, 14 Oct 2018 23:02:30 +0200 Subject: [PATCH 1/3] Add no-hybrid long-read assembly --- assembly_stats/canu.tsv | 3 +++ assembly_stats/miniasm.tsv | 2 ++ 2 files changed, 5 insertions(+) create mode 100644 assembly_stats/canu.tsv create mode 100644 assembly_stats/miniasm.tsv diff --git a/assembly_stats/canu.tsv b/assembly_stats/canu.tsv new file mode 100644 index 0000000..e29cbc9 --- /dev/null +++ b/assembly_stats/canu.tsv @@ -0,0 +1,3 @@ +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.contigs 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 +shigella_sonnei.abe 3 3 3 1 1 1 229880 229880 229880 215774 215774 215774 3 215774 229880 229883 44.99 215774 215774 215774 215774 1 1 1 1 0.00 diff --git a/assembly_stats/miniasm.tsv b/assembly_stats/miniasm.tsv new file mode 100644 index 0000000..0d58caf --- /dev/null +++ b/assembly_stats/miniasm.tsv @@ -0,0 +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 +shigella_sonnei.abe 3 3 3 1 1 1 229880 229880 229880 215774 215774 215774 3 215774 229880 229883 44.99 215774 215774 215774 215774 1 1 1 1 0.00 From d1062efa4c96627a8cdb147610aced520b13f945 Mon Sep 17 00:00:00 2001 From: Marijon Pierre Date: Sun, 14 Oct 2018 23:07:38 +0200 Subject: [PATCH 2/3] Correct error in miniasm report --- assembly_stats/miniasm.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/assembly_stats/miniasm.tsv b/assembly_stats/miniasm.tsv index 0d58caf..eb70570 100644 --- a/assembly_stats/miniasm.tsv +++ b/assembly_stats/miniasm.tsv @@ -1,2 +1,3 @@ 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 +lr 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 shigella_sonnei.abe 3 3 3 1 1 1 229880 229880 229880 215774 215774 215774 3 215774 229880 229883 44.99 215774 215774 215774 215774 1 1 1 1 0.00 From b179423304348f373247b8faf966032d02b2b21f Mon Sep 17 00:00:00 2001 From: Marijon Pierre Date: Sun, 14 Oct 2018 23:52:54 +0200 Subject: [PATCH 3/3] Fixed error in quast run --- assembly_stats/canu.tsv | 5 ++--- assembly_stats/miniasm.tsv | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/assembly_stats/canu.tsv b/assembly_stats/canu.tsv index e29cbc9..9e132bd 100644 --- a/assembly_stats/canu.tsv +++ b/assembly_stats/canu.tsv @@ -1,3 +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.contigs 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 -shigella_sonnei.abe 3 3 3 1 1 1 229880 229880 229880 215774 215774 215774 3 215774 229880 229883 44.99 215774 215774 215774 215774 1 1 1 1 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 diff --git a/assembly_stats/miniasm.tsv b/assembly_stats/miniasm.tsv index eb70570..bac0ad0 100644 --- a/assembly_stats/miniasm.tsv +++ b/assembly_stats/miniasm.tsv @@ -1,3 +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 -lr 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 -shigella_sonnei.abe 3 3 3 1 1 1 229880 229880 229880 215774 215774 215774 3 215774 229880 229883 44.99 215774 215774 215774 215774 1 1 1 1 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 -