Introduction to gFACs

gFACs is a filtering, analysis, and conversion tool to unify genome annotations across alignment and gene prediction frameworks. It was developed by Madison Caballero and Dr. Jill Wegrzyn of the Plant Computational Genomics Lab at the University of Connecticut.

Find gFACs on GitLab and read about it on bioRxiv!

Current version: 1.1

Comments? Questions? Email me at Madison.Caballero@uconn.edu

Getting started

• Installation
• Supported Input Formats
• About

Running gFACs

• Filter flags
  • Basic flags
    • -p [prefix]
    • --false-run
    • --no-processing
    • --no-gene-redefining
    • --rem-3prime-incompletes
    • --rem-5prime-incompletes
    • --rem-all-incompletes
    • --rem-monoexonics
    • --rem-multiexonics
    • --min-exon-size [number]
    • --min-intron-size [number]
    • --min-CDS-size [number]
    • --unique-genes-only
  • EnTAP required flags
    • --entap-annotation /path/to/your/final_annotation.tsv
    • --annotated-all-genes-only
    • --annotated-ss-genes-only
  • Fasta required flags
    • --fasta /path/to/your/nucleotide/fasta.fasta
    • --canonical-only
    • --rem-genes-without-start-codon
    • --allow-alternate-starts
    • --rem-genes-without-stop-codon
    • --allowed-inframe-stop-codons [number]
    • --splice-table
    • --nt-content
• Output flags
  • Basic output flags
    • --statistics
    • --statistics-at-every-step
    • --create-simple-gtf
    • --create-gff3
  • Fasta required output flags
    • --get-fasta-with-introns
    • --get-fasta-without-introns
    • --get-protein-fasta
    • --create-gtf
  • Distributions flags
    • --distributions [option] [option] …
    • exon_lengths
    • intron_lengths
    • CDS_lengths
    • gene_lengths
    • exon_position
    • exon_position_data
    • intron_position
    • intron_position_data
  • Compatibility flags
    • --compatibility [option] [option] etc…
    • SnpEff

Support scripts

• format_diagnosis.pl