Modules and tools ideas

[FernandoDuarteF]

See genomeqc ideas spreadsheet.

Genome only

• BUSCO. Genome completness. Can be run on "genome" only mode (runs Augustus first) or in "protein" mode (fasta with protein sequences).

• QUAST. Assembly contiguity (e.g. N50).

  • Also accepts GFF as input, but AGAT gives more complete statistics.

• HITE. Calculation of Transposable element content.

  • Not in nf-core

• SVbyEye. Structural variation among whole genome assemblies.

• TIDK. Telomere repeat identification.

  • Subworkflow

• LAI. Continuity of LTR sequences.

• NCBI FCS GX. Foreign contamination

• Merqury. Phasing assessment

• PLOTSR. Chromosome level summary synteny.

• MUMMER/DOTPLOT. Sequence level synteny.

• TEsorter. Captures TEs in protein domains.

• Asmgene. For evaluating gene completeness and duplication.

• calN50.js. Calculating N50 and L90

  • Probably redundant.

Annotation only

• AGAT. Genome basic statistics (gene length averages, etc).
• GenomeTools (Optional?).
• pangene. Gene variability using miniprot output.
• Liftoff. Lifting annotations

Genome and Annotation

• Orthofinder. Phylogenetic trees (or a better program, PHY… ).
• MCSCanX. Synteny between two genomes (or other program).
• GENESPACE. Runs everything that the above does.