Contig Assembly

Contig assembly is done with the ctx31 contigs command, followed by the ctx31 rmsubstr command to remove contigs that are substrings of other contigs.

Contigs are given a confidence score between 0 and 1. This is one minus the probability of missing a read that would contradict the assembled contig. It is a conservative score and gives the probability of a missing a read during sequencing, assuming the contig is not correct and the missing read would have told us. We get a confidence score for each side of a contig.

In addition to a confidence score, we also get the reason the contig assembly stopped. This is one of:

• FailNoCovg - no coverage
• FailNoColCovg - coverage in population but graph forks and sample has no coverage in any nodes
• FailNoPaths - fork in sample and no paths
• FailSplitPaths - oldest paths split at fork
• FailMissingPaths - a fork where one node has no path information

Contig scaffolding is left as an exercise for the reader.