Galaxy | Tool Preview

seqwish (version 0.7.5)
Limit transitive closure to include no more than N copies of a given input base
This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments.

These seq**uences **wish they were squished into a graph.

seqwish implements a lossless conversion from pairwise alignments between sequences to a variation graph encoding the sequences and their alignments. As input we typically take all-versus-all alignments, but the exact structure of the alignment set may be defined in an application specific way. This algorithm uses a series of disk-backed sorts and passes over the alignment and sequence inputs to allow the graph to be constructed from very large inputs that are commonly encountered when working with large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.