de novo assembly applications

Question

Hey I hope this question supposed to be in this forum.

I'm not from the biology community, I'm from the data security community so im not familiar with the words you might use for answers

I need to use an algorithm that very similar to the de novo assembly algorithm. I'll try to explain myself better I've some sequences of '1' and '0' all of them are pieces of one big sequence.

I've seen some applications that work with this algorithm such as SPAdes tadpole and Geneious but i couldn't make any of them to work for me except the Geneious because it was the simplest.

Geneious is not good for me because i need something that i can use by command line in the terminal what application do you recommand me to use that i give input the sequences and the output will be the big sequence.

BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'

Thank you very much wait for your answers :))

Answer 1

You can try Velvet, but you'll likely end up with thousands of contigs unless your expected reference genome is pretty simple. This question hits many of the difficulties with de novo assembly. I'm also not sure what you mean by this:

BTW, in the Geneious I've used a FASTA file for my sequence where my '0' and '1' translated to 'C' and 'D'

Are you trying to use this for a purpose other than actual genome assembly? You say you're from the data security field, so it's unclear what's your end goal. If you only have a binary sequence, you better have a really long read length and hope there aren't too many repeats or you'll really have issues finding a consensus sequence.