hybpiper‐nf and paragone‐nf: Containerization and additional options for target capture assembly and paralog resolution

Abstract Premise The HybPiper pipeline has become one of the most widely used tools for assembly target capture data phylogenomic analysis. After production locus sequences and before phylogenetic analysis, identification paralogs is a critical step ensuring accurate inference evolutionary relationships. Algorithmic approaches using gene tree topologies ortholog groups are computationally efficient broadly applicable to non‐model organisms, especially in absence known species tree. Methods Results We containerized expanded functionality both groups, providing novel options treatment sequence data, allowing seamless use outputs former as inputs latter. Singularity container presented here includes all dependencies, corresponding pipelines (hybpiper‐nf paragone‐nf, respectively) implemented via two Nextflow scripts easier deployment vastly reduce number commands required their use. Conclusions hybpiper‐nf paragone‐nf easily installed provide user‐friendly experience robust results community. They by Australian Angiosperm Tree Life project. available at https://github.com/chrisjackson-pellicle/hybpiper-nf https://github.com/chrisjackson-pellicle/paragone-nf .