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Releases: soedinglab/metaeuk

MetaEuk Release 7-bba0d80

30 May 09:04
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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

Metaeuk Release 6-a5d39d9

11 Jul 09:42
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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

Metaeuk Release 5-34c21f2

15 Sep 14:30
34c21f2
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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

Metaeuk Release 4-a0f584d

08 Jan 10:52
a0f584d
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Bugfix

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

Metaeuk Release 3-8dc7e0b

23 Oct 11:47
8dc7e0b
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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.

MetaEuk Release 2-ddf2742

07 Apr 11:33
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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

MetaEuk Release 1-ea903e5

28 Nov 16:25
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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

MetaEuk Release 0-c87cf06

25 Nov 16:08
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Pre-release

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