Improvement on 10X assembly using Supernova

[xingwu2]

Hello Volodymyr,

I did a 10X genomics genome assembly using Supernova, the program released by the 10X company. I want to use the architect to improve the quality of the assembly. I used BWA-MEM to align all the pair end reads, the same set used for making the assembly, to the assembly. The alignment rate was 96%. However, when I used the pe-connections.py to calculate the edges, the program outputted 0 connection. Here is the output: #Strange reads (skipped): 0 #Reads whose mate was not good: 3839735 #Read paired that were used: 0 #Connections established: 0 Do you have any idea why this happened?

Thank you

Xing Wu Graduate Student University of Illinois at Urbana Champaign