Features

• Added an option to scan for an ATG (methionine) before prediction start, if it wasn't matched (#43)
• Extended and updated README

Bug fixes

• Removed confusing MMseqs2 parameter --add-orf-stop (#88)
• taxtocontig respects --threads during the last createtsv step

Developer

• Updated to latest MMseqs2 commit

Breaking changes / Known issues

• Remove --add-orf-stop MMseqs2 parameter that was breaking MetaEuk

Features

• Added an option to collect sub-optimal exon sets
• Added exon numbers to GFF output (#36)
• Extended and updated README
• Updated MMseqs2 version

Bug fixes

• Fixed order of columns in GFF output (#36)

Breaking changes / Known issues

• Please let us know if you notice any issues

Features

• Additional output file in GFF format (#4, #32, thanks to @Andy-B-123)
• An option to print information about the position of stop codons by setting --write-frag-coords 1 (#21)
• Extended and updated README
• Updated MMseqs2 version
  • MacOS binaries are now universal (should be faster on ARM Macs)
  • Added precompiled binaries for more platforms (Linux ARM64, PPCLE64, old SSE2 machines)
  • If you are unsure which one you need it's probably metaeuk-linux-avx2.tar.gz (Linux) or metaeuk-osx-universal.tar.gz (MacOS)

Bug fixes

• --compressed parameter should not break workflows anymore (#20)

Breaking changes / Known issues

• Filename of precompiled MacOS binaries has changed (metaeuk-osx-universal.tar.gz)
• Please let us know if you notice any issues

Bugfix

• Fix FASTA header coordinates in case of an exon overlap on the minus strand (#13)

Breaking change

MetaEuk returns both the nucleotide and protein sequence of a prediction.

A call with the output basename predsResults

metaeuk easy-predict contigsFasta/contigsDB proteinsFasta/referenceDB predsResults tempFolder

will result in predsResults.fas (protein sequences), predsResults.codon.fas and predsResults.headersMap.tsv

Features

We are curently working on the taxtocontig taxonomy annotation workflow for the predictions.

Features

• Added an annotation mode to assign taxonomic labels to contigs based on predicted proteins

Fixed Bugs

• MetaEuk always uses the slice-search profile search mode to avoid accidentally using up all memory and crashing
• Docker works again

Features

• Introduced easy-predict workflow that takes FASTA contigs as input and returns FASTA predictions as output.

Fixed Bugs

• MetaEuk could crash in the last stage (unitesetstofasta) if it was run on a subset of the reference database and no predictions were produced for some contigs

At a glance: MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs.