I have NextSeq and MiSeq PE data which i have assembled using Newbler v2.6, CLC and velvet. The best assembly was obtained from Newbler. I have extracted the scaffolds related to mitochondrial origin of consisting mitochondrial gene using mitofy and BLASTN.
But now i have scaffolds. Can anyone suggest any approach to make it circularized. I am trying BBcontignet which is very complex.
Dear Ghosh,
As you said that you have already assembled the raw reads into contigs using Newbler, so I think the ABACAS package (http://abacas.sourceforge.net/) may be suitable for your subsequent connection.
Breifly, the input to ABACAS is a set of contigs, which will be aligned to the reference genome (if avaliable), and then ordered and orientated based on the alignment. The final result will be a single genome sequence with gaps.
To close the gaps, you can use the GapCloser package developped by BGI (http://soap.genomics.org.cn/about.html) with the raw sequencing reads. After that, the remaining gaps may have to be closed by PCR experiments.
Hope this will help you.
All the best,
En-Hua Xia
I have tried ABACAS but i donot have any closely related reference. I got very little alignment.
Have you a sequence identity at both extremities? If not, clearly, you need to perform a PCR and sequence by Sanger.
I have not tried PCR and sanger yet. Can you suggest if BBcontignet method will be right to be considered. As i have paired end reads.
Hi, I developed a new assembler for plastids and it should assemble the mitochondrial genome in one circular contig, at least if there is enough data.. So for which species is it and what's the size of your data files? I will upload the assembler in the next few weeks if you would be interested: https://github.com/ndierckx/NOVOPlasty
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