Hi Bastien and Miraistas,
I got some strange results comparing assemblies of newbler and MIRA. I
assembled de novo 620000 unpaired 454 Titanium reads, from a bacteria
that is ~50% GC and 5.3 Mb long.
I was expecting an average coverage of ~45X, roughly 200 long contigs,
and that's more or less what I got with Newbler (2.5.3) using standard
settings (except long contigs, which I set to 500 bp):
- almost all reads aligned
- 217 contigs > 500 bp
- N50 at 80kb, largest contig 225kb
- total size about 5.3 Mb
When I ran mira 3.4rc2:
mira --project=$ASS_ID --job=denovo,genome,normal,454 -OUT:ora=yes
-DI:trt=/scratch/tmp -GE:not=12 > assembly_log.txt &
Result was... not that good. In short:
- about 67% of reads assembled (only)
- average coverage 21 (half as expected)
- 5577 contigs > 500 bp
- N50 at 2 kb, largest contig at 18kb
- total size about 8.3 Mb (40% more than true length)
I attach the length vs coverage plot of the Mira assembly. The assembly
log is 16Mb once bzipped, so I can't send it, but I can put it somewhere
on the net if necessary.
I took exactly the same starting material. I extracted the sequences
from the sff using sff_extract with -c (or -C, can't remember) option to
hard-clip sequences. I'm running the same assembly using Mira 3.2.1.
It's in pass 2 now, but from the results of pass 1 it doesn't look very
different...
Anyone has seen this before? Mira used to perform better than newbler,
but here I'm a bit speechless...
Thanks for any idea, opinion!
Cheers,
Lionel
In details:
Newbler:
numberOfReads = 614615, 614189;
numberOfBases = 258203857, 249060819;
readStatus
numAlignedReads = 601557, 97.94%;
numAlignedBases = 239458446, 96.14%;
inferredReadError = 0.41%, 985238;
numberAssembled = 306880;
numberPartial = 294629;
numberSingleton = 1675;
numberRepeat = 169;
numberOutlier = 4549;
numberTooShort = 6287;
largeContigMetrics
numberOfContigs = 217;
numberOfBases = 5330283;
avgContigSize = 24563;
N50ContigSize = 80240;
largestContigSize = 224866;
Q40PlusBases = 5328574, 99.97%;
Q39MinusBases = 1709, 0.03%;
MIRA:
Assembly information:
=====================
Num. reads assembled: 414749
Num. singlets: 0
Coverage assessment (calculated from contigs >= 5000):
=========================================================
Avg. total coverage: 20.20
Avg. coverage per sequencing technology
454: 21.00
Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 7
Length assessment:
------------------
Number of contigs: 5577
Total consensus: 8561693
Largest contig: 18136
N50 contig size: 2088
N90 contig size: 691
N95 contig size: 604
Coverage assessment:
--------------------
Max coverage (total): 56
Max coverage per sequencing technology
454: 71
Quality assessment:
-------------------
Average consensus quality: 76
Consensus bases with IUPAC: 17498 (you might want to check these)
Attachment:
E112_11NrM01_length_vs_coverage.png
Description: PNG image
