Version 1.11

Minor update:

• Configuration file template fixed to provide path to protein sequence of a related species (rather than genome and annotation).
• Fixes issues with mac installation script.

Version 1.10

Major updates include:

• Support for single end reads
• Protein sequence of a related species should be supplied rather than related species genome and annotation
• Multiple related species can not be used
• Option to scaffold/combine reference genes together based on de novo assembly sequence (off by default)
• De novo assembled sequences are split, if they are found to match multiple (separated) protein sequences from a related species. This overcomes de novo assembled sequences being thrown out if they are "false chimeras".
• Samples are mapped separately to the reference genome in the genome-guided assembly step. This allows users to compare to a "reference only" analysis if they wish, or to visualise read alignments against the genome etc.

Version 1.01

Minor update for installation scripts. This version will install Lace version 1.13 which contains some bug fixes and is faster to run.

Version 1.00

Adds more options:

• Trintiy, StringTie, HISAT2, blat and featureCounts options can not be ued
• Pre generated assemblies can now be passed to Necklace to bipass assembly.

Necklace version 0.9

The first release of necklace.