NAME

       art - Artemis genome browser and annotation tool

SYNOPSIS

       art [options] SEQUENCE_FILE [+FEATURE_FILE...]

OPTIONS

               SEQUENCE_FILE                  An EMBL, GenBank, FASTA, or GFF3 file
               FEATURE_FILE                   An Artemis TAB file, or GFF file

               -options FILE                  Read a text file of options from FILE
               -debug                         Run using the debugging JVM instead
               -fast  |  -fast64                 Use  the  FastVM  (hp Tru64 UNIX) with 32/64 bit
       pointers

               -Dblack_belt_mode=?            Keep warning messages to a minimum [true,false]
               -Doffset=XXX                   Open viewer at base position XXX [integer >= 1]
               -Duserplot=FILE[,FILE2]        Open one or more userplots
               -Dloguserplot=FILE[,FILE2]     Open one or more userplots, take log(data)
               -Dbam=FILE[,FILE2,...]         Open one or more BAM, VCF or BCF files
               -DbamClone=n                   Open all BAMs in multiple (n > 1) panels
               -Dbam[1,2,..]=FILE[,FILE2,..]  Open BAMs in separate panels
               -Dshow_snps                    Show SNP marks in BamView
               -Dshow_snp_plot                Open SNP plot in BamView
               -Dshow_cov_plot                Open coverage plot in BamView
               -Dshow_forward_lines=?         Hide/show forward frame lines [true,false]
               -Dshow_reverse_lines=?         Hide/show reverse frame lines [true,false]
               -Dchado="h:p/d?u"              Get Artemis to open this CHADO database
               -Dread_only                    Open CHADO database read-only

EXAMPLES

               % art AJ006275.embl
               % art contigs.fa +annotation.gff +islands.tab
               % art -Dblack_belt_mode=true -Dbam=ecoli_hiseq.bam E_coli_K12.gbk
               % art -Duserplot=repeatmap.plot,geecee.plot Plasmid.gff3

SEE ALSO

               http://www.sanger.ac.uk/resources/software/artemis/

       act(1), dnaplotter(1)

                                          February 2014                                    ART(1)