[mira_talk] no singletons in 454 assembly
- From: Peter Menzel <pmenzel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 8 Oct 2012 16:20:15 +0200
Hi.
I am using mira 3.9.4 for assembly of 454 reads from some metagenomes.
So far, mira makes makes longer contigs than Newbler, but for some reason
mira seems to never report singleton reads (neither in the
*.info_assembly.txt file nor in the *.unpadded.fasta output files).
So I wanted to ask if this is a known behaviour or maybe a bug?
For example, one data set contains 707,206 reads and newbler has
110,635 singletons and Celera has 46,346 singletons left.
Mira reports:
Num. reads assembled: 645541
Num. singlets: 0
So there must be some reads left as singletons?
The file *_info_debrislist.txt has 132545 entries.
I found similar behavior for other 454 assemblies as well.
thanks, Peter
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