Yes, I used the long option described at the github page - should have been more explicit about that in original post.
Tony said that this should work for PB reads, but it has not worked as well as I (we) expected. I’m moving the twitter-based discussion over here with the thought that somebody may benefit from the discussion.
About mapping - Heng Li has done a lot of engineering with the recent versions of BWA to allow for the mapping of very long reads. While I think Heng and Mark and the the PB people can argue about the best mapper, `bwa mem -x pacbio` is not too shabby. I’d be happy to modify the abyss-pe makefile to use blasr, but I don’t think that is the issue, given that the SAM file contains a lot of successfully mapped reads.
Happy to share whatever data is helpful in solving this issue. I think there are lots of people who would scaffold with PB reads using ABySS if it worked well enough.
Matt