Description

Validate, filter, convert and perform various other operations on GFF files

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing meta data
e.g. [ id:‘test’ ]

gff (file)

A reference file in either the GFF3, GFF2 or GTF format.

*.{gff, gtf}

fasta (file)

A multi-fasta file with the genomic sequences

*.{fasta,fa,faa,fas,fsa}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing meta data
e.g. [ id:‘test’ ]

gtf (file)

GTF file resulting from the conversion of the GFF input file if ‘-T’ argument is present

*.{gtf}

gffread_gff (file)

GFF3 file resulting from the conversion of the GFF input file if ‘-T’ argument is absent

*.gff3

gffread_fasta (file)

Fasta file produced when either of ‘-w’, ‘-x’, ‘-y’ parameters is present

*.fasta

versions (file)

File containing software versions

versions.yml
included in
atacseq chipseq hicar nascent riboseq rnadnavar rnaseq rnasplice rnavar scrnaseq
maintainers
Github user edmundmiller
Github user gallvp
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gffread
MIT

GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more.

http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread https://github.com/gpertea/gffread 10.12688/f1000research.23297.1