GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html Note: This was the original repository which will no longer be officially maintained. Please use the new official repository here:
I have Oxford Nanopore data of a bacterium. I am mapping the reads to an assembly of the same identical strain to check the assembly.
If I use the standard alignment alogrithm (anchor) all works fine.
However, if I use "anchorgotoh" it get the exception "std::bad_alloc". I have to say that we have a lot of really long reads (>400kb).
ghost
commented
6 years ago
I have Oxford Nanopore data of a bacterium. I am mapping the reads to an assembly of the same identical strain to check the assembly.
If I use the standard alignment alogrithm (anchor) all works fine. However, if I use "anchorgotoh" it get the exception "std::bad_alloc". I have to say that we have a lot of really long reads (>400kb).
Is this a known problem? How can I help to debug?