Releases · ncbi/egapx

New features integrated from RefSeq EGAP:

ortholog analysis vs a pre-defined reference species
refinement of gene biotype (protein-coding, pseudogene, lncRNA) based on annotation and orthology properties
Assignment of gene symbols, names, and protein names based on orthology or comparison to SwissProt proteins
Better annotation of single-exon protein-coding genes based on well supported proteins
Automatic selection of organism symbol format, ortholog reference species, protein reference sets, maximum intron size, and some annotation-related parameters
Added target protein sets for plant clades and additional vertebrates
Integration of structural and functional annotation into final output, including: ASN.1, GFF, GTF, mRNA FASTA, CDS FASTA, protein FASTA

Execution improvements:

Added versioning for EGAPx (egapx.py runner, Docker/Singularity images)
Added check for user input files
Improved support for pre-download of reference files
Updated STAR to produce csi index instead of bai index to work for large sequences
Increased time limit for chainer
Updated chunk size for miniprot tasks to 25k
Enable skipping gnomon training when parameters from closely-related taxa are available
Relocated Python requirements.txt to repo root

Future plans:

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