[mira_talk] Re: large number of contigs
- From: John Nash <john.he.nash@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Wed, 31 Oct 2012 15:43:39 -0400
17-fold coverage for 454 is way too low. Try 40-fold.
On 2012-10-31, at 3:20 PM, "Bahr, Sarah" <sarah-bahr@xxxxxxxxx> wrote:
> 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)
--
You have received this mail because you are subscribed to the mira_talk mailing
list. For information on how to subscribe or unsubscribe, please visit
http://www.chevreux.org/mira_mailinglists.html
Other related posts:
