contigs alignment with long reads

Question

[midox]

Hello,
I have contigs generated by an assembler and I have long reads DNA.
I want to make a contig alignment with long reads, I want to develop an alignment program.
Before doing that, I need to know conernant contigs.
do I have to consider their orientation? or I can used on the long reads without problems?
thanks

[midox]

any response? thanks

[Chris Cole]

You're wanting to develop something that already exists e.g. blasr, Last, bwa mem. Why not use them instead? The existing tools work very well, are free and open source.

If you really want to develop a new tool, you're best reading up on how the existing tools work and get answers to your specific questions there.

[midox]

no, there is no tool that can do what I want. alignment tools use all sequences in a file. But I want to use each sequence of each file. so there are no tools that can do what I want.

[Biomonika (Noolean)]

You need to be more specific. How did you get your long reads? Which assembler did you use, what was the input data for the assembler and how many contigs do you have? Do you want to align each of your contigs on (one of) the long reads?

[midox]

for the assembler, I am trying to test to see the results. yes I want to align contigs file on the long file reads. can I get a simple alignment without treatment on contigs?

and can you explain me the orientation of contigs? do we use the orientation of contigs to form the scaffold only?

thanks

[Biomonika (Noolean)]

You can blasr or bwa mem to do that. Regarding contig orientation - if this is an assembly from genomic DNA - you won't know which strand you assembled. So it can be the sequence as it is or its reverse complement.

[midox]

no, blast and bwa mem take the two files. They do not take each sequence of each file. yes, I have DNA sequences. So, I can align contigs on a long reads without treatment. am I right?

[Biomonika (Noolean)]

What do you mean by developing an alignment program? Do you want to compete with long reads aligners like blasr or bwa mem?

[midox]

I want to align contigs on long reads. I do treatments on long reads.

but I wanted to know I take the contigs without making changes? I use the file "contigus.fa"?

I think there is an orientations in the contigs and I do not know what that means!!(can you explain me this?)

So, I can make the alignment directly or I do modifications?

thank you for your explanations