Arda Söylev

Thanks so much Fritz, Sorry but I'm not clear about the question 2; I want to test my algorithm with a simulated data. So, I want SURVIVOR to add the...

I have one last question, I'm using grch37, which is haploid, so what happens when I set "NUMBER_haploid" to 2. Since the genome is not diploid, it has no effect...

Oh sorry, yes you are right. I was expecting to see "_maternal", "_paternal" added to the header of the chromosomes in the fasta file so I hadn't gone to the...

With lower bandwidth it got resolved but I cannot regenerate this issue currently. I will let you know if I see this again but now I have a similar issue...

Actually this is not for a specific scenario; I'll use it in my algorithm and currently testing it with ONT data of some samples (reads can be retrieved from the...

I'm also sending a sample cluster of reads. This is one of the large clusters (25 reads), so not all of them are that large. [H2-s218243_1350.fasta.zip](https://github.com/yangao07/abPOA/files/15175950/H2-s218243_1350.fasta.zip)

I actually want to generate a consensus but since the poa algorithms are slower, I had to use wtdbg2. Your algorithm seems to be much faster, so I wanted to...

Hi, It's a naming that we used for the variants. To be more precise, for a variant such as "**chr1-21837-COMPLEX->s65863s1192-104**": The convention that we used is: **_chromosome name - position...

Can you send me some lines from your GAF and GFA? e.g., **cat sample_aligned.gaf |head -n 5000 >dnm.gaf**

We do not output SV breakpoints but you can use an assembly based SV discovery tool such as SVIM-asm or PAV for this (by giving the svtigs as input).