Thank you for this awesome tool! Our group is currently constructing de novo assemblies using ~100x 150bp paired short illumina reads + matched HiC ~5kb resolution.
We first construct contigs using abyss 2.0 with bloom filter which produced highly fragmented assemblies ( n50 ~ 33000 and ~2000000 contigs). Given that yahs requires smaller number of input contigs, we opted to use ragtag patch to improve contiguity, which significantly improved assembly statistics, as expected (n50 ~ 137.5e6 and ~ 11186 scaffolds). We used the outputs of ragtag for yahs but it didn't really improve our assembly statistics (n50 ~ 128e6 and #scaffolds ~ 11059).
I'm wondering if 1. using scaffold outputs from ragtag is an appropriate input for yahs? and 2. if you have any suggestions to improve this pipeline.
Thank you again for this awesome tool!
Eunice
Thank you for this awesome tool! Our group is currently constructing de novo assemblies using ~100x 150bp paired short illumina reads + matched HiC ~5kb resolution.
We first construct contigs using abyss 2.0 with bloom filter which produced highly fragmented assemblies ( n50 ~ 33000 and ~2000000 contigs). Given that yahs requires smaller number of input contigs, we opted to use ragtag patch to improve contiguity, which significantly improved assembly statistics, as expected (n50 ~ 137.5e6 and ~ 11186 scaffolds). We used the outputs of ragtag for yahs but it didn't really improve our assembly statistics (n50 ~ 128e6 and #scaffolds ~ 11059).
I'm wondering if 1. using scaffold outputs from ragtag is an appropriate input for yahs? and 2. if you have any suggestions to improve this pipeline.
Thank you again for this awesome tool!
Eunice