What can AGAT do for you?

AGAT a GFF/GTF toolkit allowing you to perform almost everything you might want to achieve ^^

AGAT has the power to check, fix, pad missing information (features/attributes) of any kind of GTF and GFF to create complete, sorted and standardised gff3 format. Over the years it has been enriched by many many tools to perform just about any tasks that is possible related to GTF/GFF format files (sanitizing, conversions, merging, modifying, filtering, FASTA sequence extraction, adding information, etc). Comparing to other methods AGAT is robust to even the most despicable GTF/GFF files.

Standardize/sanitize any GTF/GFF file into a comprehensive GFF3 format (script with _sp_ prefix)

task	tool
check, fix, pad missing information into sorted and standardised gff3	`agat_convert_sp_gxf2gxf.pl`

  * add missing parent features (e.g. gene and mRNA if only CDS/exon exists).  
  * add missing features (e.g. exon and UTR).  
  * add missing mandatory attributes (i.e. ID, Parent).  
  * fix identifiers to be uniq.  
  * fix feature locations.  
  * remove duplicated features.  
  * group related features (if spread in different places in the file).  
  * sort features (tabix optional).  
  * merge overlapping loci into one single locus (only if option activated).  

Convert many formats

task	tool
convert any GTF/GFF into BED format	`agat_convert_sp_gff2bed.pl`
convert any GTF/GFF into GTF format	`agat_convert_sp_gff2gtf.pl`
convert any GTF/GFF into tabulated format	`agat_sp_gff2tsv.pl`
convert any BAM from minimap2 into GFF format	`agat_convert_sp_minimap2_bam2gff.pl`
convert any GTF/GFF into ZFF format	`agat_sp_gff2zff.pl`
convert any GTF/GFF into any GTF/GFF (bioperl) format	`agat_convert_sp_gxf2gxf.pl`
convert BED format into GFF3 format	`agat_convert_bed2gff.pl`
convert EMBL format into GFF3 format	`agat_convert_embl2gff.pl`
convert genscan format into GFF3 format	`agat_convert_genscan2gff.pl`
convert mfannot format into GFF3 format	`agat_convert_mfannot2gff.pl`

Perform numerous tasks (Just about anything that is possible)

task	tool
make feature statistics	`agat_sp_statistics.pl`
make function statistics	`agat_sp_functional_statistics.pl`
extract any type of sequence	`agat_sp_extract_sequences.pl`
extract attributes	`agat_sp_extract_attributes.pl`
complement annotations (non-overlapping loci)	`agat_sp_complement_annotations.pl`
merge annotations	`agat_sp_merge_annotations.pl`
filter gene models by ORF size	`agat_sp_filter_by_ORF_size.pl`
filter to keep only longest isoforms	`agat_sp_keep_longest_isoform.pl`
create introns features	`agat_sp_add_introns.pl`
fix cds phases	`agat_sp_fix_cds_phases.pl`
manage IDs	`agat_sp_manage_IDs.pl`
manage UTRs	`agat_sp_manage_UTRs.pl`
manage introns	`agat_sp_manage_introns.pl`
manage functional annotation	`agat_sp_manage_functional_annotation.pl`
specificity sensitivity	`agat_sp_sensitivity_specificity.pl`
fusion / split analysis between two annotations	`agat_sp_compare_two_annotations.pl`
analyze differences between BUSCO results	`agat_sp_compare_two_BUSCOs.pl`
... and much more ...	... see here ...