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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 ...