How can I run Necklace with multiple related species?

Combine the fasta sequence of all related species. eg. cat human.prot.fa mouse.prot.fa > all.related.prot.fa Then provide all.related.prot.fa in the configuration file.

Can I run Necklace without a related species, for example on human?

Yes, the workaround here is to specify human as the related species, as Necklace expects a file to be provided. On species such as human, the pipeline has the potential to find novel gene annotations (such as novel exons), but be aware that Necklace has not been designed for this type of analysis and may miss potentially interesting novel genes due to its filtering (for example fusion genes).

Can I run Necklace with a different version of Java?

As long as bpipe executes with the version of Java you have, you may still run Necklace even without Java 1.8. However, you will be required to run de novo assembly yourself (using whatever assembler you prefer) and should pass the assembly filename to Necklace (see Options).

Can I run Necklace on single end data?

Yes. Simply leave Read_R2="" in the configuration file.

Can I use Necklace with long read data?

PacBio data can be used by Necklace in place of a de novo assembly. You can achieve this by adding: de_novo_assembly_file=<pacbio.fasta> to the configuration file. We don't recommend trying this with Nanopore data due to the error rate.