NAME

       act - Artemis comparison tool for genome sequences

SYNOPSIS

       act [options] SEQUENCE_1 COMPARISON_1_2 SEQUENCE_2 ...

OPTIONS

               SEQUENCE                   An EMBL, GenBank, FASTA, or GFF3 file
               FEATURE                    An Artemis TAB file, or GFF file
               COMPARISON                 A BLAST comparison file in tabular format

               -options FILE              Read a text file of options from FILE
               -chado                      Connect to a Chado database (using PGHOST, PGPORT, PGDATABASE, PGUSER
       environment variables)

               -Dblack_belt_mode=?         Keep warning messages to a minimum [true,false]
               -DuserplotX=FILE[,FILE2]    For sequence 'X' open one or more userplots
               -DloguserplotX=FILE[,FILE2] For sequence 'X' open one or more userplots, take log(data)
               -DbamX=FILE[,FILE2,...]     For sequence 'X' open one or more BAM, CRAM, VCF, or BCF files
               -Dchado="h:p/d?u"           Get ACT to open this CHADO database
               -Dread_only                 Open CHADO database read-only

EXAMPLES

               % act
               % act af063097.embl af063097_v_b132222.crunch b132222.embl
               % act -Dblack_belt_mode=true -Dbam1=MAL_0h.bam -Dbam2=MAL_7h.bam,var.raw.new.bcf
               % act -Duserplot2=/pathToFile/userPlot

SEE ALSO

               https://sanger-pathogens.github.io/Artemis/ACT/

       art(1), dnaplotter(1)

                                                 September 2020                                           ACT(1)