[mira_talk] Singlets after hybrid assembly
- From: Andrew Gracey <mirabilis@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 5 Sep 2009 22:18:49 -0700
Hi Folks/Bastien,
I'm an absolute beginning user and my question is about singlets or the lack
thereof in the results of a recent assembly. I have ~170K 5' and 3' Sanger
reads and ~1 million FLX 454 reads from a eukaryote transcriptome. First of
all I assembled just the Sanger reads to verify that MIRA was working and I
got a nice assembly of 28,389 contigs and singlets. Then I tried a hybrid
assembly which ran for >48hr on a 64-bit 24Gb Linux box. But the assembly
yielded just 5,495 contigs (147,039 reads were in the contigs) and I can't
find my singlets? The manual mentions the following option:
*savesimplesingletsinproject(sssip)=**on|yes|1,off|no|0* Default is *no*.
Controls whether 'unimportant' singlets are written to the result files.
What's the definition of 'unimportant' and can this explain why I didn't get
any singlets written in the output files?
These are the call parameters that I used
./mira -project=Bot -job=denovo,est,normal,sanger,454
I have fasta and qual files for the sanger data, and the 454 data were
extracted using the sff_extract script.
Below I've pasted what was in my assembly info file.
Thanks in advance for any insights you can offer.
Andrew
Localtime: Sat Sep 5 07:28:45 2009
Assembly information:
=====================
Num. reads assembled: 1079084
Num. singlets: 2340
Large contigs:
--------------
With Contig size >= 500
AND (Total avg. Cov >= 3
OR Cov(san) >= 0
OR Cov(454) >= 3
OR Cov(sxa) >= 0
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 30951
Total consensus: 37182812
Largest contig: 9906
N50 contig size: 1352
N90 contig size: 685
N95 contig size: 620
Coverage assessment:
--------------------
Max coverage (total): 4780
Max coverage
Sanger: 367
454: 6169
Solexa: 0
Solid: 0
Avg. total coverage (size >= 5000): 10.29
Avg. coverage (contig size >= 5000)
Sanger: 0.49
454: 8.89
Solexa: 0.00
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 70
Consensus bases with IUPAC (IUPc): 96774 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 186 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 208 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
All contigs:
------------
Length assessment:
------------------
Number of contigs: 75734
Total consensus: 67118803
Largest contig: 9906
N50 contig size: 961
N90 contig size: 507
N95 contig size: 450
Coverage assessment:
--------------------
Max coverage (total): 4780
Max coverage
Sanger: 367
454: 6169
Solexa: 0
Solid: 0
Avg. total coverage (size >= 5000): 10.29
Avg. coverage (contig size >= 5000)
Sanger: 0.49
454: 8.89
Solexa: 0.00
Solid: 0.00
Quality assessment:
-------------------
Average consensus quality: 57
Consensus bases with IUPAC (IUPc): 202037 (you might want to
check these)
Strong unresolved repeat positions (SRMc): 186 (you might want to
check these)
Weak unresolved repeat positions (WRMc): 212 (you might want to
check these)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 14 (you might want to check
these)
Contigs with reads wo qual values: 3 (you might want to check
these)
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