Unicycler v0.4.1

Small changes and bug fixes:

• Tweak logic to better include plasmids in the final assembly, even when the Illumina assembly graph is weird (thanks Matthew Croxen)
• Makefile fix which caused some people to have compilation issues with zlib (thanks @tomasyeo, @andersgs and @swlong)
• Made compilation less specific to avoid problems in heterogeneous environments (thanks @cerebis)
• Fixed potential issues with read name parsing (thanks @cerebis)
• Set a SPAdes thread limit to avoid memory issues (thanks @ConstantinV)
• Better error messages with bad Illumina input reads (thanks Gabriele Margos)
• Ability to manually set multiplicities in the Illumina graph, to override Unicycler's multiplicities when you think it's made a mistake
• Efficiency improvements in assembly graph manipulations

Unicycler v0.4.0

This release contains lots of changes and improvements! Some highlights:

• Unicycler can now assemble long-read-only data using a miniasm+Racon pipeline.
• Hybrid assemblies use this new long-read-only functionality to better handle low-quality Illumina reads.
• New bridge type added, simple long read bridges, to better handle two-way junctions and loops.
• The read depth filter has been relaxed (was previously too aggressive) and exposed as an option: --depth_filter.

Other bug fixes include:

• Fix polishing problem when assembling unpaired Illumina reads.
• Fix crash with duplicate read names in FASTA read input (occurred with Canu-corrected reads).
• Avoid BLAST crash due to threading (affects some BLAST versions).
• Fix alignment failure due very long, perfect alignments.

Unicycler v0.3.1

A few small improvements and fixes:

• Bug fix for read alignment crash
• Fix BLAST issue with space-containing directory paths
• Add table of program dependencies to stdout
• Other stdout tweaks

Unicycler v0.3.0

Plenty of improvements in this release:

• Improved alignment algorithm, especially for reads with repeated sequence
• Bug fix for Unicode related crash
• Better handling of the Pilon executable
• And lots more!

Unicycler v0.2.0

Beta release!

Unicycler v0.1.0

First alpha release of Unicycler.