Hi everybody , i did one listeria genome assembly with Spades and scaffolding through Abacas. The pseudo genome i got from Asbacas it has few gap and i want to fill this gap can anybody suggest me any suitable software to do this job. Thank you.
If you are already using PAGIT, there is a program called IMAGE that is for extending contigs and removing gaps. In addition, you may want to try GapFiller or GapCloser in the SOAPdenovo package. One important point to consider is that ABACAS is not a scaffolding program, it is for ordering/orienting contigs relative to a reference. It may be advisable to run an actual scaffolding program before trying to close gaps in the assembly, or just use IMAGE, depending on the goal of your study.
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version 2.3.6
I tried with IMAGE but i did not find any suitable manual for that. I have only two read file one reference genome and one Scaffolding file i dont know how to use all this in IMAGES and for GapCloser : can i use as a third party program , means if i do assembly with other than SOAPdenovo can i still use this package?? and for scaffolding could you please suggest me some reliable program.
My best advice is to do a quick search of the forum or the web. Normally I don't say that, but there are many of discussions on scaffolding on this site and I could not do it justice in a comment.