A never version of the pipeline is now up at the repository. This version helps with OS X compatibility and provides a workaround for a newly discovered bug in FreeBayes.
The reference contigs now have a single N placed on both 5’ and 3’ ends of the contig. The current version of FreeBayes was ignoring some reads that mapped exactly to the 5’ end of a reference contig, and adding the N padding fixes this issue.
Also, dDocent now outputs the reference in the correct orientation. Previous versions output reverse complemented reference contigs. This had no impact on SNP calling; it’s just important to note for comparisons to previous runs.
It is recommended that all previous analyses are rerun with the current version. The new version will most likely result in more SNP calls with higher coverage.