[mira_talk] large number of contigs
- From: "Bahr, Sarah" <sarah-bahr@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 31 Oct 2012 19:20:17 +0000
Hello,
I am finding that every time I attempt to assemble my genome I am getting a
large number of contigs. Any advice on what may be the issue?
Thanks,
Sarah
Localtime: Wed Oct 31 10:18:12 2012
Assembly information:
=====================
Num. reads assembled: 281466
Num. singlets: 0
Coverage assessment (calculated from contigs >= 5000):
=========================================================
Avg. total coverage: 17.43
Avg. coverage per sequencing technology
Sanger: 0.00
454: 17.78
IonTor: 0.00
PcBioHQ: 0.00
PcBioLQ: 0.00
Text: 0.00
Solexa: 0.00
Solid: 0.00
Large contigs (makes less sense for EST assemblies):
====================================================
With Contig size >= 500
AND (Total avg. Cov >= 6
OR Cov(san) >= 0
OR Cov(454) >= 6
OR Cov(ion) >= 0
OR Cov(pbh) >= 0
OR Cov(pbl) >= 0
OR Cov(txt) >= 0
OR Cov(sxa) >= 0
OR Cov(sid) >= 0
)
Length assessment:
------------------
Number of contigs: 703
Total consensus: 9852494
Largest contig: 108574
N50 contig size: 25927
N90 contig size: 7074
N95 contig size: 4188
Coverage assessment:
--------------------
Max coverage (total): 137
Max coverage per sequencing technology
Sanger: 0
454: 137
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 0
Solexa: 0
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 81
Consensus bases with IUPAC: 341 (you might want to check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
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: 829
Total consensus: 9966183
Largest contig: 108574
N50 contig size: 25581
N90 contig size: 6649
N95 contig size: 3580
Coverage assessment:
--------------------
Max coverage (total): 137
Max coverage per sequencing technology
Sanger: 0
454: 137
IonTor: 0
PcBioHQ: 0
PcBioLQ: 0
Text: 0
Solexa: 0
Solid: 0
Quality assessment:
-------------------
Average consensus quality: 80
Consensus bases with IUPAC: 377 (you might want to check these)
Strong unresolved repeat positions (SRMc): 0 (excellent)
Weak unresolved repeat positions (WRMc): 0 (excellent)
Sequencing Type Mismatch Unsolved (STMU): 0 (excellent)
Contigs having only reads wo qual: 0 (excellent)
Contigs with reads wo qual values: 0 (excellent)
Other related posts:
