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ART(1) General Commands Manual ART(1)


art - Artemis genome browser and annotation tool


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


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


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


act(1), dnaplotter(1)

February 2014