I have contigs after sequencing. How to combine them as single and find the genes? Are there free tools for this analysis?
Please elaborate what kind of data you have and from which sequencing platform
I dont completely understand whether you have contigs or raw reads. If you have raw reads in .fastq format you need to assess the quality, trim it and then assembly it.
If you have already assembled the sequence and you have contigs you will have to convert into scaffolds first. You may use Scaffold builder (http://edwards.sdsu.edu/scaffold_builder/) provide you have a reference for that. It also depends on the kind of data that you have and the sequencing platform used. If the data and coverage is less you will need to do gap closing in order to get a whole genome or whatever it is that you have sequenced.
@Ayachit - As of now we are doing scaffolding and annotation. The problem is after even annotation we could not get the sequential arrangements of contigs/scaffolds. If you could give some info on that, it will be helpful
If you there is a closely related genome already published you can use this with Mauve to order the contigs. But this will only be a prediction, you will have to confirm by PCR
I agree with Andrew above. Besides this, before checking the order, first you can verify the quality of your assembly. You need to map your assembly back on the raw reads to see how much of raw reads have been used (Use BWA). Also if this is a eukaryote you can use CEGMA or BUSCO for checking assembly.
- Badges
- Science topic
- Similar topics
- Philosophy
- Moral Philosophy
- Free Will