Is there a closely related organism that has been previously fully sequenced and closed? If so, you can use that sequence as a reference and align your contigs to it to create a single scaffold. I recommend MAUVE. Within the software is a 'reorder contigs' function. Drag and drop your reference fasta file and then the fasta file of your 50 contigs. Make sure that the reference file is list FIRST on the Mauve screen. Then hit reorder. It will go through multiple iterations and come up with a final 'best' ordered. You can save the final ordering, remove the indicators between the contigs and use that to create your circular map. Mauve will not calculate gaps that might exist between your contigs but it will provide a best estimate of how your contigs should be ordered in the final scaffold.

http://darlinglab.org/mauve/download.html

Contiguator can do the same thing: http://contiguator.sourceforge.net/

To merge the ordered contigs you can as Brittan mentions manually delete the indicators (i.e., all lines beginning in ">" except the first one).

Or if you are on the command line type:

grep -v ">" multisequence.fasta > merged.fasta

Then manually add back a indicator line  using a text editor at the very beginning of the file e.g. ">Merged Anoxybacillys flavithermus AK1 genome" 

Hello Brittan

Thank you for your reply.I think its really helpful.

Yes, there is a reference sequence available. It is Anoxybacillus flavithermus WK1.

http://www.ncbi.nlm.nih.gov/genome/1710?genome_assembly_id=171558

In my case, I have Anoxybacillus flavithermus AK1. However, as I mentioned I have 50 contigs. Now, I will follow your instructions and will try to do it. One last thing, how I can remove the indicators? is there any option in the sofware itself?

Thanks

For contig assembly just use SSPACE.

SSPACE is not working anymore

Mauve is the best as the guys said, to remove the indicators either manually using any text editor or using the grep -v command as Patrick Degnan said.

How can i remove contaminant from whole genome sequencing

@Bukola, submit the assembled genome to NCBI/Genbank and they will do that for you

@Bukola Aremu: Use KRAKEN2. It will detect contamination of sequences from bacterial, archaeal, viral, as well as human genomes, or custom genomes provided.

https://github.com/DerrickWood/kraken2

Irene Aldea Ramos You can do this easily in R or using python script. Ask someone who can write script for you. But i must tell you that its not correct strategy.

Irene Aldea Ramos you probably shouldn't do that. If the file comes from an assembly, the contigs are contigs because the assembler cannot determine how they are related. And you don't know anything about their contiguity.

Hello Irene Aldea Ramos, if your contigs are from assembly, you may first try to order your contigs using MAUVE and a close reference genome. In next steps, using the ordered contigs you may try for 'scaffolding' using SSPACE followed by polishing with GapFiller tool of the same software. This scaffold fasta file may be submitted to NCBI or may be included stretches of several 'NNNNs' between contig gaps and at the end of sequence to form a 'circular molecule'.

Regarding answer to your query, to join the contigs you may use online FaBox tool to concatenate your fasta sequences into one which will remove all the internal headers with '>' symbol.

hello, Could you please suggest to me, any bioinformatics software/tool for synteny analysis of my nematode genome. I've tried so many software but they are very troublesome and some of them are actually not working. I would greatly appreciate it if you kindly advise me on this!

And also, is Mauve working in Windows Microsoft? I can't download it....

You might try "RagTag" python program. It is available through conda.